One North Korean fisherman was killed and eight others were injured during the deadly incident on Friday evening.
Russia’s Federal Security Service (FSB) said the trawler, named Dae Yong No. 10, had crossed into Russian waters while fishing in the Sea of Japan.
The Russian patrol ship fired warning shots, which were ignored by the North Korean fishermen who continued to operate in the area.
FSB officers then boarded the ship and discovered “illegally obtained aquatic bio-resources”.
They said the fishing crew responded aggressively to the discovery and attempted to escape.
When this proved fruitless, they attacked the guards and attempted to take their weapons.
The Russians then shot the boat’s engine before turning their guns on the threatening North Korean fishermen.
One FSB officer received a head injury during the fight, according to a statement released by the guards after the incident.
The FSB said: “During the search and control activities, FSB guards found illegally-obtained water bio resources on board the vessel.
“The ship’s crew behaved aggressively towards members of the search group, refusing to comply with legal requirements.”
There were 48 North Koreans on board the fishing boat during the incident. A Russian doctor remained on board with the fishermen and provided medical support while the boat was brought to a Russian port in the Primorsky Territory.
The wounded have now arrived at the Nakhodka port, where the FSB said “an investigation will be carried out”.
Relations between North Korea and Russia have historically been generally friendly, especially during the cold war.
However, relations are becoming increasingly strained between the two states, with 60 per cent of Russians now believing Kim Jong-un’s nuclear arms pose a threat to other country.