The head of Hiyoshi Suisan, the company that owns the Yoshi Maru No. 38, said an agreement had been reached with the Russian authorities concerning the sum of the bail and fine.
"The money has been transferred today," said. "All the 10 people, including the captain, will be released next week, the ship will also be returned to us."
The crabbing vessel was intercepted by the Russian Coast Guard on January 27 near the northern coast of the Noto Peninsula on suspicion of illegal fishing in what Russia calls its exclusive economic zone.
A catch of crabs was found onboard, the ship's captain had no documentation proving the ship had permission to catch crab in the area. The vessel was escorted to Russia's Far Eastern port of Nakhodka for further investigation.
Hiyoshi Suisan previously dismissed Russia's claims and said the vessel may have inadvertently entered Russian waters after completing its fishing operations.
Confrontations over poaching between Russian authorities and Japanese fishing vessels are frequent in Russia's Far East. In August 2006 a Japanese fisherman was shot dead near the Kuril Islands - some of which are claimed by Japan - when Russian border guards opened fire on his boat after it failed to stop.