The clash, which occurred on Tuesday, follows a string of earlier incidents involving North Korean fishermen.
Crew members of a North Korean vessel have attacked Russian border guards in the Sea of Japan, wounding three servicemen, Russia's Federal Security Service (FSB) told Russian state news agency TASS on Tuesday.
The FSB security service, which controls the border and coast guard, said in a statement that guards observed two fishing vessels and 11 motor boats while on duty in Russian waters of the Sea of Japan.
In a separate statement, the Russian Foreign Ministry said it summoned the North Korean charge d'affaires to personally lodge a protest with Pyongyang.
"On August 23 and 24, the patrol boat and ships of Japan Coast Guard were chased out by the self-defensive measures of the DPRK when those made illegal intrusion into our exclusive economic zone", the spokesperson said, using the acronym for Democratic People's Republic of Korea, North Korea's official name.
North Korea also seized a Russia-flagged ship with 15 Russians and two South Koreans in July, but released the boat and its crew days later.
Writing for NK News in December a year ago, North Korea watcher Andrei Lankov noted how the DPRK's fishermen often head further afield in search of more abundant fishing grounds. Last week, border guards detained 16 boats and over 250 sailors who were poaching squid off Russian shores.
There are frequent disputes over fishing rights in the Sea of Japan that is surrounded by Japan, Russia and both North and South Korea.
Russian Federation says they were caught in its Exclusive Economic Zone, which extends 200 nautical miles (370km) from its coast.