Russia detained three North Korean vessels and 252 crew on Friday in the second such incident in two weeks as part of a clampdown on poaching by the secretive nation's fishermen.
The detentions mark rare confrontation between North Korea and Russia, which sees itself as an important player in international talks on defusing nuclear tensions around the reclusive state's missile programme.
Border guards impounded the vessels in waters off Russian's far eastern coast that Moscow considers its exclusive economic zone, the Interfax news agency reported.
Border guards said they had seized more than 30,000 squid and illegal fishing equipment and were holding the vessels and several motorboats at the port of Nakhodka, the report said.
The Kremlin said the move would not damage its ties with Pyongyang.
"A lot of North Korean poachers cross Russia's border and poach illegally in Russian territorial waters so of course energetic measures are needed to impose order in this area," Kremlin spokesman Dmitry Peskov said.
North Korea, which is reeling under sanctions over its weapons programme, has struggled with food shortages and a dysfunctional state rationing system for years.
Its crop production this year is expected to drop to its lowest in five years, bringing serious shortages to 40% of the population, the United Nations said last week.
Russia detained two North Korean boats in its territorial waters in the Sea of Japan on Sept. 17 after one of them attacked a Russian patrol.
In that incident, Russia said it detained a vessel for poaching, prompting a second boat to open fire. Several border guards and alleged poachers were hurt and one of the North Koreans later died from his wounds.
Moscow summoned a North Korean diplomat over the incident.
A regional border official at the Federal Security Service said last week the poachers had resisted because they feared punishment back home for loss of state property over the confiscation of their vessel.
The countries have had disputes over fishing in the region in the past. Moscow accused Pyongyang in July of illegally detaining one of its fishing vessels. North Korea said the crew had been detained for breaching the rules for entering its territory.