There is another fisheries dispute based on contested sovereignty. This time it is between South Korea and Japan. The dispute is over the Liancourt Rocks, called Dokdo by the Koreans and Takeshima by the Japanese. Sounds like the Japanese may be pushing there claims on the waters sounding these rocks which the South Koreans have been administering since 1954.
To give you an idea how seriously the the South Koreans take this dispute, the largest warship in the South Korean Navy, an 18,000 ton big deck amphib, is named Dokdo.
This and other disputes, are why it is so difficult for these two countries, which would appear to be natural allies, find it so hard to work together.
Chuck Hill's CG Blog 
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Here’s an interesting commentary from the -new- Defending Japan blog. This incident occurred just as Japan was approaching South Korea about working together on defense strategies and logistics sharing.
“The timing of this incident could not be worse.”
“Of course, it is safe to assume that the timing is no coincidence either.”
“All it takes is one fervent nationalist in a fishing boat to stir up some tension, and the house of cards could all come crashing down.”
S Korea and Japan: Hopes Dashed?
On the other hand, looks like they are handling this professionally. The way I read Google earth it looks like when the S. Koreans learned about it the boat was in waters SK claims as their EEZ, but if the violation occurred earlier in waters that SK also views as Japanese EEZ there may be no real conflict–you took a chance and you got caught. “If you can’t do the time, don’t do the crime.”
More commentary on this conflict:
http://newpacificinstitute.org/asw/?p=10440
This is not going away. The Japanese hoped to have it arbitrated, but the S. Koreans have refused.
http://www.globalsecurity.org/military/library/news/2012/08/mil-120822-voa01.htm?_m=3n.002a.588.jj0ao001ud.j70