Papua, Jayapura: Clearing into Indonesia here

Cruisers report on checking in to Indonesia in Jayapura. Note that checking into Indonesia should now be a lot simpler with the new clearance system that is in place for pleasure yachts.

Published 8 years ago, updated 5 years ago

Jayapura: © SY Totem

See Indonesia Formalities for the latest details on checking into and out of Indonesia.

SY Adina checked in to Indonesia at Jayapura on 1st September 2015.

Jayapura is a busy city with many restaurants, ATMs and shops; for us it was it was a useful stop after time spent travelling through remote islands in Papua New Guinea.

Remember the clocks go back one hour when arriving from PNG!


Having completed departure formalities in Vanimo, PNG, we left at sunset and arrived into the bay at Jayapura before midnight. We had used satellite images to select a location away from potential hazards for a nighttime arrival. We anchored at 02 37.012 S 140 46.382 E in 7m of mud. There was some swell, but it was tolerable.

We slept here before raising the anchor at first light to motor the 6.5nm to the main harbour. We dropped anchor at 02 32.405 S 140 42.512 E in 32m of mud and plastic bags. This location is tucked into the north of the harbour, away from heavy shipping, and close to town.

On our second morning, we were woken to be asked to move closer in, as a ferry and a Navy ship were coming in. We re-anchored as close to the shore as we felt comfortable. A friend’s yacht who came in after we had left, anchored here as well and the navy actually moved their boat while they were in town! They then anchored at 02.32.548S 140.42.535E. in 28m of mud. This is further from town but removes the risk of disturbing the navy boat should it be around.

The anchorage is not very pleasant, littered with plastic bags and general debris, but the holding seemed ok.

Getting ashore

We used the Police dock (02 32.2841 S E140 42.483 E) visible nearby for our dinghy using the phrase “Boleh kami tinggal disini?”; to ask permission to leave it there. We used the dock many times and there were often different Police personnel around. We were always friendly and checked with the new personnel and never had an issue and were always given a friendly wave.

The watch-out here is that the tide gets very low, down to less than 30cm of water at the side of the dinghy dock closest to the river mouth. Once we realised this, we left our dinghy on the outer side of the dock between the large Police boats.

If you arrive needing cash, walk up to the street from the Police dock and turn right. Less than fifty metres along is the closest ATM.

Getting around

Whilst many of the distances around the city look walkable, the heat makes it challenging. Fortunately, there are many cheap mini-vans that operate as taxis: white for within the city, 3000Rp per person wherever you want to go; green for locations out of the centre, 4000Rp per person – you will need to take one of these to get to the Immigration office; blue ones are for the airport.


The best way to complete all the formalities is to start with Harbour Master, then Customs, then Quarantine and finally Immigration. The one snag here is it is difficult to pronounce the word for Harbour Master, so you may want to go to Customs first and walk back 300m to the Harbour Master. It’s a good idea to carry a boat card to show in case you get problems explaining what we needed to do; this seemed to work well given our non-existent Indonesian and most people’s limited English. A boat stamp is essential and was well used and it sped things up to have copies of all our main documents to hand over to the officials.

1. Harbour Master = “Kantor Syahbandar Dan Otoritas Pelabuhan”

Location: Jl Koti #8.

The Harbour Master is located on the road running south out of the city along the waterfront – take a taxi – you may want to go to customs as it is easier to pronounce and then walk back here – it’s around 300m from the customs office. They took copies of our boat registration document, CAIT, clearance document from Vanimo, our crew list and passports. As the officer wanted to keep the original of the clearance document from Vanimo we asked him to provide us with a copy in case we needed it to show Customs, which it turned out we did. We received no paperwork back but were asked to return before departing from the port in order to get our Port Clearance. Other yachts after us have reported being asked for bribes – refuse.

2. Customs = “Bea Cukai” (pronounced Choo-kai)

Location: On Jl Koti, further south (out of town) from the Harbour Master – about 300m.

There was a large pile of papers for us to complete. We provided copies of our boat registration document, CAIT, clearance document from Vanimo, our crew list and passports. They wanted details of all our boat equipment including navigation systems, computers, liferaft etc. but never checked the detail which was good as we didn’t know the serial numbers off all our equipment. They also want details of alcohol/tobacco onboard.

We asked about the need for a temporary import permit (PIB) and were told that yes, we needed to have one and that they could not be issued in Jayapura but in Sarong or Biak. We asked the officer to stamp and sign the letter we had produced ourselves for our PIB in case we had an issue in the meantime. This letter, which you can do yourself, simply states that you will not engage in commercial activities or sell your boat.

Having completed the paperwork we were told we would need to return to the office before leaving the port to collect our completed arrival papers from him. The officers also wanted to inspect Adina in person, which we arranged for later that day. The inspection was quite thorough, rummaging around under the sinks, looking

under the floorboards and in most cupboards, but there were no issues.

To note, when we got to Sarong we were told that the letter we had with Jayapura customs’ stamp and the signature was all we needed for the PIB, and there was nothing more the Sarong office would issue. We produced it when we checked out in Belitung and had no problems.

3. Quarantine = “Kesehatan Pelabuhan”

Location: On Jl Koti, 100 metres south from Customs, 02 32.798S 140 42.786E.

We were immediately shown into a car and driven out of the city up to another facility where the relevant officer was working. He completed the paperwork very quickly and efficiently, providing us with a receipt for the 40,000Rp fee for the Certificate of Practice. The paperwork required from us was the boat papers, CAIT, passports and crew list. Again we were asked to return before departing the port in order to obtain a Quarantine Port Clearance. Both of these documents were needed for our clearance out of Indonesia.

4. Immigration = “Kantor Imigrasi”

Location: Jl Fery, Cepos Lama Kelapa II, Entropy, 2.34.0399S 140.42.1039E.

This was the most challenging of all formalities, purely because the office had recently moved out of the city and few people seem to know about this! To get to the new office you need to take a green mini-van to Entropy which is an area on the outskirts of Jayapura. The journey takes about 15 minutes and costs 4000Rp per person. The office is down a side street and not obvious. We suggest writing the address on a piece of paper to show the driver. If he cannot find it, ask him to go to the Papua New Guinea Embassy which is nearby – the gentleman working there knew where to find the Immigration office. Another option that worked for friends after us is when you have finished at Quarantine, give the officers there the address and get them to get you a taxi and explain it to the driver.

Having already obtained our Social Visas in Vanimo (PNG), once at immigration we needed to fill in an arrival card and provide copies of our boat registration, CAIT, crew list and passports. Once our passports had been stamped, we were asked to go and get copies of the visa and entry stamp for Immigration to keep – there was no photocopy machine in the office. There are plenty of photocopy shops around, we just asked to be shown to the nearest one. Immigration will give you a blank departure card and a stamped crew list – hold on to this,

you will need it to clear out.

5. Police = “Polisi”

Location: Polresta, Jl Yani 11 (in the centre of town), 02 32.573S 140 42.231E.

As we were planning a couple of stops in Papua we needed to get a “Surat Jalan”, a tourist permit for the region. We went to the Central Police Station (“Polresta”), asked at the reception for a “Surat Jalan” and were shown to the correct office. We needed to provide copies of our passports, visas and entry stamps, two passport photos per person, the boat papers and our CAIT. The officer asked for a “contribution to the administrative costs”. We asked if there would be a receipt for the contribution, to which the answer was “no”, so we politely declined. This caused no issue. We went to a photocopy shop and made five copies of the “Surat Jalan” in the expectation we would need them in other towns, as advised by the officer.

You will need one of these letters if visiting Raja Ampat.

As an aside, in the alleyway opposite the Polresta, there were numerous stalls making rubber stamps to requirement.

Diesel = “Solar”

Technically you are now allowed to take your own jerry cans to a petrol station and get fuel, but this is a new law and slow to filter out to all the islands. When we were in Jayapura the law had yet to be introduced. Having got chatting to the Police officers at the dock, we asked about obtaining “solar” and were introduced to Selfi, one of the officer’s wives. She was able to help us obtain diesel at a price of 11,000Rp per litre. We tried to negotiate, but there was no budging, so given we wanted to be in Jayapura as short a time as possible we went ahead. We felt if we had moved to an anchorage out of the main harbour we might have found it easier

to find someone who would sell us diesel for a more reasonable price – you should be able to get it from a fisherman for 10,000Rp per litre. Be warned this fuel is not the cleanest – so use filters. Overall we found Selfi helpful, but pushy. She is keen to work with yachts and can be contacted on +62 812 40882018.


After visiting various shops with Selfi we established that gas bottles cannot be refilled in Jayapura, only exchanged.


There is a hypermarket in the Jayapura Mall which is within walking distance of the Police dock. Go up to the street and turn left, follow to the main road, look to the right across the crossroad and you will see Jayapura Mall. The hypermarket is in the basement. We found the stock to be adequate to restock on a few things we were missing, including decent beef and chicken (no pork or lamb available). In the Mall, you will also find various clothes and electronics shops with items at good prices.

On departure

We revisited Quarantine, Customs and the Harbour Master in that order to complete departure formalities, taking just over two hours in total. The resulting documents all cleared us to our next port in Indonesia, Sarong. They would not clear us to our final port in Indonesia, insisting we had to stop in Sarong.

Useful phrases

Salam = Hello

Terima Kasih = Thank you

Selamat tinggal = Goodbye (when you are leaving)

Di mana…? = Where is….?

Di mana Kantor Imigrasi? = Where is the immigration office?

Boleh kami tinggal disini = Can I leave the dinghy here?

Heading on

You do not need to go to Sarong and may prefer to skip yet another dirty harbour and head straight to Waisai (00 25.831S, 130 49.422E). Provisioning is better in Sarong and fuel probably a little cheaper. But you can get fuel in Wasai and provision there. And Raja Ampat is where you want to be.

Tom and Susie

Yacht Adina, London

SY Totem checked in to Indonesia in Jayapura in December 2012.

Here is a bit of practical information I hope will be helpful for boats clearing into Indonesia at Jayapura, Papua. A more informal review of our experience of clearing in is on the Sailing with Totem blog at


Our initial anchorage near police docks was at 2*32.406 S, 140*42.558E. This is deep (90’) but convenient to the main part of town.  We also anchored at 2*33.039, 140 43.2485 E- south of town- after our formalities were completed. This is on the south side of two islets with stilt villages; other boats have anchored on the north side of those islets, which is convenient to the customs and quarantine locations.

At the first anchorage, look for a dock at the N end of the bay with a smaller police boat or two tied up to it. This is a helpful place to come ashore. Ask the guys on the dock nicely (Boleh kami tinggal disini?) and they’ll let you leave the dink or do a drop-off. The lovely families in the laneway to the left of the police dock will also look after your dinghy for you, and you may be directed to tie up there instead.

We later moved to the more southern waypoint. Watch for reefs you must go around to tuck into this spot. The water was much cleaner here, so we could run our watermaker again- simply not possible in the very

foul water at the first anchorage. This is closer to the Hamadi neighbourhood which has a thriving open market. Lots of curious and friendly Papuan families from the adjacent stilt village stopped by. Very little English spoken so it really helps to have a couple of phrases to use. OK, almost no English is spoken except “Hey Mister” (universally applied to men and women).

Clearing in:

This took us 2 days but considering the amount of bureaucracy involved this ends up feeling fairly efficient. Naturally, these offices are all in different parts of town. At least the “taksi” service (actually a shared minivan used for public transportation) is cheap- about US$0.20 for a ride across town.

The police dock is the closest point to immigration for leaving your dinghy- see the Lonely Planet map (our 2007 edition showed the location accurately) or ask anyone “di mana Kantor imigrasi?” We acquired social visas at the Indonesian Consulate in Vanimo prior to arrival, with our ship’s agent providing the sponsorship for the 60-day visa. After the initial grant, these are later renewed at monthly (not 60 days) increments.

Customs and quarantine are adjacent to each other, near the dock for the Pelni ferries. Take a taxi and ask for the “Dok Pelni”, headed toward Hamadi from downtown- 2,000 Rp. Use the English word for customs, but Quarantine is easier to find by asking for the Indonesian “Kesehatan Pelabuhan”. Quarantine is located about 100 meters south down the road from customs. Quarantine wanted Rp 50,000 and- to our surprise- vaccination records for everyone on board: we haven’t been asked for that before and cobbled one together from existing records.

The Harbormaster was offended that we did not visit their offices first; it is located on the road towards town from the customs and quarantine offices.

You’ll want a boat stamp. Officials were visibly dismayed when we didn’t have a stamp, although only one insisted we delay paperwork until I brought out a stamp from the boat. New stamps can be cheaply made at Gramedia, a bookshop on the waterfront. Anyone can direct you there. This is a great place to pick up a pocket-sized English/Indonesian dictionary or regional maps.

Surat Jalan (travel letter – a permit specific to travel in Papua):

Coming west from PNG, make sure to get a surat Jalan after you arrive in Jayapura. This letter is a police clearance used in Papua to keep track of expats and is a product of the ongoing Free Papua Movement.

There was a heightened concern during our visit and the police were very serious about this paperwork being acquired. I don’t believe you can get one in advance, only in Jayapura. The police facility where this

is acquired is adjacent to the police dock anchorage- go left when coming ashore there. It seems boats coming from the east aren’t always required to take this step, but we most certainly were. We think we

look pretty innocent, but Totem received a great deal of military attention during our <1-week stay, probably because expats have been implicated in trafficking for the Free Papua Movement. Spare yourself the interrogation we had with the intelligence police and approach them within a day of your arrival.

Boat inspection:

We weren’t inspected. Customs officials stopped by the boat, on their way to a shooting range (!), while Jamie and the kids were aboard and I was ashore at immigration with all our paperwork. The customs guys

just wanted to make sure we planned to clear in; this was as close as any officials ever came to boarding Totem. However, we most definitely felt watched by officials for the duration of our stay. There is a clearly significant concern with the current violence in the Free Papua Movement. It is occasionally uncomfortable, as we were approached several times.

Getting online:

Galilea Computer, behind the post office, sells broadband modems that work across a variety of services. Get the modem there, but then go purchase a SIM card and high-speed data plan from Telkomsel: a large

Telkomsel office is just up the road from Galilea towards town. The data bundled with the modem runs out quickly and is effectively useless (sold as “unlimited” but so slow, it’s not functional, making

this two-step process necessary). Data plans are 30 days and readily recharged around the country.


The local subsidized price for gas or diesel at the time of our visit was 4500 Rupiah/litre, or about US$0.45. You cannot legally purchase this subsidized fuel, but someone will do it for you for a markup. Just keep asking (you will probably be approached) and eventually you’ll get hooked up. Depending on how much you need, a payoff to the police is involved as well. We had offers to help acquire from several people (including government officials!) but many of them weren’t actually able to follow through despite apparent good intentions.


Many local groceries have all the basic staples. There’s an upscale grocery store near immigration with imported goods. Look for the big KFC restaurant signage; it’s on the ground floor underneath the restaurant. It was nice to restock on things like olives, capers, muesli and peanut butter after a few months of yams and coconuts. The Hamadi public market is the best place for fresh produce, but a smaller market exists in town as well.


SY Totem

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