Russian coastguards say they have seized two North Korean boats and more than 80 crew members.
Russia said the ships were engaged in illegal fishing off its coast, and that one of the vessels launched an "armed attack".
Three Russian border guards were reportedly wounded in a clash.
North Korea has yet to comment on the incident, but Russia's Foreign Ministry has expressed "serious concern" and summoned the country's top diplomat.
A spokesperson for the Russian Federal Security Service (FSB) said the two schooners were accompanied by 11 motorboats and were spotted poaching near the Yamato Bank, which lies between the Korean Peninsula, Russia and Japan.
Russia says they were caught in its Exclusive Economic Zone, which extends 200 nautical miles (370km) from its coast.
The detained vessels are being taken to Russia's Far East port of Nakhodka, Interfax news agency reported, quoting the FSB.
This is not the first time the countries have had run-ins in the region.
North Korea has previously seized Russian boats. In July, it arrested a fishing crew.