The boat left after Japan posted a bond of US$390,000 under a settlement by an international tribunal, a foreign ministry statement said. The Hoshin Maru No 88 was seized on June 1 off Russia's far eastern Kamchatka peninsula on charges of poaching.
The boat was due to arrive on Sunday at a port on Japan's northern island of Hokkaido, the statement said. Russia and Japan frequently have disputes over fishing rights, with Russian coast guard ships often moving in on Japanese trawlers.
The Hamburg-based International Tribunal for the Law of the Sea last week ordered Russia to free the trawler upon Japan posting bond.
The two countries have never signed a peace treaty formally ending World War II, as Japan claims four islands off its northern coast which Soviet troops seized days after Tokyo's surrender.