Two Russian fighter jets violated Japanese airspace on Thursday with Tokyo scrambling jets in response, the defence ministry said.
The Russian planes were detected off the coast of northernmost Hokkaido island for just over a minute, shortly after Japan's new prime minister said he wants to find a "mutually acceptable solution" to a decades-old territorial row with Russia and sign a long-delayed peace treaty with Moscow.
Japan's foreign ministry lodged a formal protest over the incursion by a pair of Russian SU-27 fighters at about 3:00 pm local time (0600 GMT).
"Today, around 3:00 pm, military fighters belonging to Russian Federation breached our nation's airspace above territorial waters off Rishiri island in Hokkaido," the foreign ministry said.
The incident came hours after hawkish Japanese premier Shinzo Abe -- who swept to power in December with pledges to get tough on diplomacy -- offered apparently conciliatory comments toward Moscow over the Russian-administered Southern Kurils, known as the Northern Territories in Japan.
Abe's tone was in marked contrast to his uncompromising stance on a dispute with Beijing over the sovereignty of a different set of disputed islands.
"There is no change in my resolve to do everything I can towards sealing a peace treaty with Russia after resolving the issue of the Northern Territories," Abe said.
In December, Abe and Russian President Vladimir Putin agreed to restart talks on signing a peace treaty formally ending the hostilities of World War II that has been stymied by the dispute.
"In the telephone talks, I told President Putin I would make efforts to find a mutually acceptable solution so as to ultimately solve the issue of the Northern Territories," Abe told a government-backed rally of around 2,000 former islanders and their descendants in Tokyo.
Soviet forces seized the isles, which stretch out into rich fishing waters off the northern coast of Hokkaido, in the dying days of WWII and drove out Japanese residents.
The islands were later re-populated by Russians but remain a poor and undeveloped part of the country.
Abe's comments come as tensions between Japan and China have intensified over the sovereignty of the Tokyo-administered Senkaku Islands in the East China Sea, claimed by Beijing as the Diaoyus.
On Tuesday Japan said a Chinese frigate had locked its weapons-targeting radar onto a Japanese military vessel, the first time the two nation's navies have locked horns in a dispute that flared badly last summer.
Abe on Wednesday called the radar move "dangerous" and "provocative".
The Japanese prime minister has repeatedly said there is no room for negotiation over the East China Sea islands. But he has also stressed the row should not harm overall ties with Beijing, an important trading partner.