Japan - Clearance

Initial entry into Japan must be made at an official Port of Entry.

Japan Pre-Arrival Procedures for Yachts

Pre-Arrival Procedure Form (PAPF)

The JCG (Japan Coastguard) requires all vessels to submit a Pre-Arrival Procedure Form (PAPF) 24 hours in advance, but at least a week in advance is strongly recommended and greatly appreciated by officials. The PAPF (in English) can be downloaded from the Japan Coastguard website and faxed or emailed (jcgbnahakq3-8f5m@mlit.go.jp) to the relevant JCG office.

Submitting a detailed crew list, including nationality and passport information, is strongly recommended; sending copies of all passports will also help expediate the clearance process.

The PAPF is designed for commercial vessels, so don't worry too much if you can't fill in all the boxes. The JCG are good at answering emails and use an online translator.

The form requires that you specify a date and time of arrival. It is obviously difficult to know exactly what that will be far in advance, so just write down your best guess.

Advance Notice of Arrival

Forty eight hours (48) hours before arriving, email the JCG office and give them an exact day/time of arrival - and then - arrive at precisely that time, slowing down if necessary!

Twenty (plus) officials (who are used to handling punctual commercial vessels) will be waiting on the dock to give you a “royal welcome” and so don’t arrive 15 minutes early or late! Try to arrive between 09:00 and 16:00, preferably on a weekday; if clearing in at a marina, don’t arrive on the marina’s weekly holiday (usually Tuesdays, but confirm in advance).

It is recommended to request the JCG to arrange a moorage location with the port authority of your chosen POE, as they probably don't speak English. Also confirm with the JCG that they will notify Customs, Quarantine and Immigration on your arrival, and ask JCG to notify Customs that you will be applying for a Naikosen (see below).

A Closed Port Permit can also be applied for in advance of arriving in Japan (see further details below).

Japan Ports of Entry for Yachts

There are approximately 150 ports of entry in Japan, however, Noonsite only covers those that are commonly used by cruising boats.

A full list of Open Ports (Open Port = clearance port) might be helpful [https://www.mlit.go.jp/common/001257673.pdf]. However, bear in mind that not all of the ports on this list offer 24/7 clearance services. Some don’t have officials based there, so they can only clear in/out a vessel if an advance request is made (and those ports tend not be very accommodating for small pleasure craft). A lot of people (20+) are involved in clearing in a boat, so it’s hard to justify moving that manpower to a port to clear in a boat with 1-2 people on board.

It's also worth noting that Quarantine, Customs, Immigration and Coast Guard each decide how to staff their own offices, with no co-ordination among them. This can mean that clearance takes a long time and travel to the airport, for example, to find Immigration may be involved. Also, some ports (especially in the north) are seasonal: fully staffed in the summer, empty in the winter.

Guidelines to Which Ports for Clearing in and out:

• For yachts going to/from Korea (and sometimes Russia), Izuhara and Fukuoka are the main options.
• For boats going to Alaska/BC/US mainland, there are four clear-out options in the northern island of Hokkaido. Kushiro is the most popular, however Wakkanai (at the far northern tip of Hokkaido) is a good option with a provisioning/preparation stop in Otaru (on the NW coast) beforehand. Hakodate is popular, especially for those going direct to Canada or Seattle, not via Alaska.
• For those entering Japan from the Aleutians, Wakkanai is the best option.
• For boats coming from the south or southeast, Yonabaru Marina on the main Okinawa island is the most familiar with international yachts for inward clearance. Many boats think that they can clear in at Ginowan Marina in Okinawa, but it’s not in an Open Port.
• When coming from the east, Chichijima, Ogasawara is a natural port of entry, however, it’s important to note that one cannot get Naikosenpaku status here and this can be problematic as should be secured at your first POE (see further details below). Better to choose Wakayama, Yokohama, or various other Open Ports along the Pacific coast.
• Yonabaru and Wakayama handle 70% of clear-ins.
• Going direct across the Pacific, one could clear out of Hyogo/Wakayama/Yokohama/Tokyo/Choshi. Clearing out of Hokkaido means you can then head east/northeast, but boats in a hurry will leave from central Japan and take the Great Circle route.

Click on "Explore Country" -  then "Main Ports" to see a list and links to the ports of entry. 

Japan Arrival Procedures for Yachts

Closed-Port Permit System

Ports in Japan are divided into closed ports and open ports. Since May 2018, foreign cruisers can apply, either before or on entering Japan, for a “blanket” closed-port permit that allows them to enter all closed ports at any time, with no expiration date (which is 98% of the country, including all anchorage spots). There is no longer any need to prepare a long list of all the intended ports of call.

There is a very simple one-page form available on the MILT website. Full details can be found at http://www.mlit.go.jp/common/001260368.pdf

The permit is valid indefinitely (as long as the boat is in Japan and its ownership, name, home address, etc. remain unchanged), with no need for permit renewals and there is no fee.

Applications can be made by e-mail, and the permit will be returned by e-mail. It can take up to a week to get the permit.

Customs Naikosen Permit

To be exempted from filing Customs paperwork in every port (open or closed) and from complying with strict Customs regulations/requirements (such as having to file paperwork for everything taken on/off the boat [even a can of Coke!] or getting advance permission for anybody wanting to board the boat [even just to drink a can of Coke!], pleasure boats can request registration as a domestic (coastal) cruising boat — “Naiko Senpaku” or "Naikosen" - on entering the first port in Japan. This is strongly recommended, but you may have to be firm and persistent in order to get it. (Note that it is not possible to get a Naikosen in Chichijima, an island south of Tokyo and a popular place for cruisers to enter Japan when coming from the east/southeast, so clearing in there is not recommended.)

Superyachts (over 24m) are now also eligible to apply for a Closed Port Permit and a Naikosen, exempting them from having to clear in/out at every port.

General Clearance Procedures

Having done the proper notifications to the local JCG office (see above), 20+ officials will be waiting at the dock for your arrival.

The formalities are time-consuming as there are lots of forms to fill in, but this is mostly routine and officials are always very friendly and courteous.

1. Quarantine:
   If planning on getting a Naikosen (see above) inform Quarantine as soon as they come on board as they may (depending on the port) need to do a more detailed inspection and give Customs a certificate that then allows them to issue a Naikosen.
   It’s best not to have any fresh fruit/vegetables, meat (fresh or frozen), and (occasionally) spices on board when arriving; if you do, they will be discarded.
   Quarantine officials will request that detailed health questionnaires for each crew member be completed and do health checks.
   There are special requirements for clearing into Japan with pets, and that can only be done at a few Open Ports; for more information see the pets section.
2. Customs:
   Will do an extensive search of the boat and have forms to fill in.
   Request a “Naikosen” to change one’s boat to domestic status for Customs purposes; that may be issued during the clear-in process, but, more commonly, one has to pick it up at the Customs office a day or two later. See Customs for more details about the Naikosen.
3. Japan Coast Guard (JCG):
   May well come with Customs and ask questions in order to fill in their forms.
4. Immigration:
   Will record fingerprints and take ID pictures, check and stamp passports and issue visas.
5. Police:
   Depending on the port and the nationalities of the boat and/or crew, local police officials may also join the clear-in process.

It is not necessary to use an agent, although they can assist with completing the advance paperwork, reserving moorage locations, and overcoming the language barrier. Even with an agent, though, there are still a lot of forms to be filled out at the time of clear-in. In total, it takes 2-3 hours to complete the clear in.

Domestic Cruising in Japan

It is not necessary to report to officials in every port, nor are you required to advise any officials of future destinations and cruising plans (although you will often be asked).

If you have a Naikosen, plus the Closed Port Permit, then cruising Japan is virtually paperwork-free.

Officially, when visiting open ports (large commercial ports), one is required to submit a port entry/exit General Declaration to the local Coast Guard office. In fact, though, many Coast Guard offices waive that requirement for smaller pleasure vessels (often boats under 20 tons).

If you do not have a Naikosen, then you may get visited by Customs as you cruise the country, perhaps at every port (open and closed), and be requested to complete a lot of paperwork each time, especially if they apply the letter of the law to you (sometimes they do, sometimes they don’t).

Last updated: January 2025