The Japanese prime minister, Junichiro Koizumi, has written to President Putin of Russia, urging him to avoid a worsening of the long-running dispute over four small islands claimed by both countries.
Mr Koizumi said Japan could not accept the Russian action in granting fishing rights around the islands to North Korean and Ukrainian vessels.
He said that if the issue remained unresolved, it could seriously affect relations between Tokyo and Moscow.
Japan claims possession of the islands off the northern Japanese territory of Hokkaido, which were seized by the former Soviet Union in the last days of the Second World War. The islands are known as the Northern Territories in Japan, and as the Kurile Islands in Russia.