The ministry said Russia had protested to Tokyo against frequent border infringements by Japanese trawlers.
"If Japan fails to take effective measures in the immediate future, rather than mere words, to prevent any violations of the [1998 fishing] agreement, Russia reserves the right to raise the issue of future fishing in the area for Japanese fishermen," the ministry said in a statement.
Confrontations over poaching between Russian authorities and Japanese fishing vessels are frequent in Russia's Pacific waters. Last August, a Japanese fisherman was shot dead near the Kuril Islands when Russian border guards opened fire at his boat after it refused to stop.
The incident further strained relations between Russia and Japan, which have contested the ownership of the Kuril Islands for over 60 years, a dispute that has kept the two countries from signing a formal peace treaty after World War II.
Last week Russian customs officers detained four Japanese fishing vessels for poaching near the South Kuril Islands, which is former Japanese territory off Russia's Pacific Coast. Inspections revealed that out of 11 boats only seven had permission to catch fish in Russian waters.
Also last week, Russia's State Fisheries Committee announced that Russia would launch a crackdown on illegal crab exports and other sea food to Pacific Rim countries from the beginning of 2008.
In 2006, a total of 80 fishing vessels made illegal catches in Russia worth over 900 million rubles ($36 million). In the last two years a total of 7 million tons of illegally-caught seafood, worth 230 million rubles ($9.2 million), has been seized in Russia's Bering and Okhotsk Seas.