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Cheapest way to get out of Japan and get back in?

Sep 26, 2018
Nobody's replying so I'll give a crack at it.

No mention of destination so I'll just give an example for Shimonoseki to Busan (Korea).

Below is the web page of the Shimonoseki Port.
Doesn't show prices for all the ferries, but 関釜フェリー has their cheapest room as 9000 yen (one way).

I also checked the website below which is a ticket booking site for ferries.

Direct Ferries

In my search for Shimonoseki - Busan, it was like 171.13 USD for a round trip. So bit cheaper to book directly.

Lastly, I checked tripadvisor for flight tickets.
Since I believe this is for the cheapest option and not about the destination, I changed the location to international airports (Fukuoka - Seoul) which will likely have more flights, hence likely be cheaper.

Cheap flights to Seoul (SEL) - TripAdvisor

At the time I searched the cheapest for Fukuoka - Seoul was 11403 yen for a round trip, so seems in a given situation, the chances are that flights could be cheaper.
JFYI, ferry takes like 8hrs, flight takes like 1hr 25mins.
May 6, 2015
Using skyscanner and hitting "anywhere" as the destination and choosing the cheapest place & day is the cheapest way.

That said keep in mind Japan is not friendly to visa running. You're limited to 6 months / year in the country.