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. 下関市港湾局:国際フェリー・RORO航路のページ
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.
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.
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.
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