Chief Cabinet Secretary Yoshihide Suga says the Japanese government lodged a protest after two suspected North Korean vessels were spotted last month in Japan's exclusive economic zone.
Suga revealed on Friday that a fisheries agency patrol ship spotted an unidentified vessel in Japan's exclusive economic zone in the Sea of Japan off the Noto Peninsula on August 23.
He said another vessel approached a Japan Coast Guard patrol ship in the same area the next day.
The Coast Guard said a man on board the vessel pointed a gun at the patrol ship from a distance of about 30 meters. It said another person on the vessel used a video camera to record the incident.
The Japanese patrol ships were not damaged.
Suga said the relevant ministries have shared information on the incident, and the Japanese government believes the vessels were from North Korea.
He said Japan lodged a protest with Pyongyang through diplomatic channels in Beijing.
North Korean and Chinese fishing boats have been illegally operating in Japan's exclusive economic zone for several years.
Suga said the relevant ministries will work closely to ensure the safety of Japanese fishing boats in the area.