The boat was stopped and inspected on Tuesday in Russia's exclusive economic zone. Border patrol officers found a catch of frozen crab.
"The captain was unable to provide documents confirming the legality of the catch," Federal Security Service border guard spokeswoman Lt. Col. Natalya Rondalyova said.
The Japanese vessel is being escorted to a port in Russia's Far East, where the captain is expected to stand trial.
Russia last year launched a crackdown on the illegal trade in crab and other seafood, with more than $6 million worth of live crabs being returned to the sea during the year.