Japan said its fighter jets used flares for the first time to warn a Russian reconnaissance aircraft to leave its airspace, the defence ministry in Tokyo said, as tensions rise over increasing Russian and Chinese military cooperation in the region.

An undisclosed number of F-15 and F-35 warplanes were scrambled and fired flares on Monday after the Russian II-38 maritime patrol aircraft apparently ignored their radio warnings, Japan’s defence minister, Minoru Kihara said.

Kihara said it was also the first publicly announced airspace incursion by a Russian aircraft since June 2019, when a Tu-95 bomber entered Japanese airspace in southern Okinawa and around the Izu Islands south of Tokyo.

He said the Russian plane had breached Japan’s airspace above Rebun Island, just off the coast of the country’s northernmost main island of Hokkaido,three times during its five-hour flight in the area.

“The airspace violation is extremely regrettable and today we lodged a very serious protest with the Russian government via diplomatic channels and strongly urged them to prevent a recurrence,” Kihara added.

The Japanese prime minister, Fumio Kishida, told government officials to respond “firmly and calmly” to the incident and work with the US and other nations, the chief cabinet secretary, Yoshimasa Hayashi, said.

“We will refrain from giving any definitive information on the intent and purpose of this action, but the Russian military has been active in the vicinity of our country since the invasion of Ukraine,” Hayashi added.

Kihara said the use of flares was a legitimate response to airspace violation and “we plan to use it without hesitation”.

The incursion came a day after a joint fleet of Chinese and Russian warships sailed around the Japanese northern coast. Kihara said the airspace violation could be related to a joint military exercise that Russia and China announced earlier this month.

Japanese defence officials are concerned about growing military cooperation between the China and Russia, and China’s increasingly assertive activity around Japanese waters and airspace. It led Tokyo to significantly reinforce defences of south-western Japan, including remote islands that are considered key to Japan’s defence strategy in the region.

Earlier in September, Russian military aircraft flew around southern Japanese airspace. A Chinese Y-9 reconnaissance aircraft briefly violated Japan’s southern airspace in late August.

The Chinese aircraft carrier Liaoning, accompanied by two destroyers, sailed between Japan’s westernmost island of Yonaguni and nearby Iriomote, entering close to Japan’s waters.

Japan’s air self-defence force said it had scrambled jets 669 times between April 2023 and March 2024, about 70% of the time against Chinese military aircraft, although that number did not include airspace violations.

Japan and Russia are in a territorial dispute over the Northern Territories, a group of Russian-held islands that the former Soviet Union seized from Japan at the end of the second world war. The row has prevented the two countries from signing a peace treaty formally ending hostilities.

Bilateral tensions have also risen over Japan’s support for Ukraine. Tokyo has offered Kyiv financial and material support and imposed sanctions on Russian individuals and organisations.