Russia said one North Korean was killed and eight others injured after a routine maritime check turned violent on Saturday.
The Russian security service, the FSB, said in a statement that border coastguards detained the boat and found "illegally obtained aquatic bio-resources."
The trawler Dae Yong No. 10 was said to have entered Russian waters in the Sea of Japan, when it was boarded.
A skirmish apparently broke out in which a member of the Russian coastguard sustained a head injury.
According to the statement, the North Korean crew "reacted in an aggressive manner with the coastguards and refused to obey the law."
The coastguard ship then fired at the trawler's propulsion system, to disable it after the crew attempted to escape with the boat. Members of the crew were also hit.
The Russian statement said the action had been taken "in legitimate self-defense."
Russia and North Korea share a short border along the River Tumen, with a maritime border dividing their territorial waters in the Sea of Japan. The two countries generally enjoy good relations.
rc/bw (AFP, AP)