Japan says two Russian fighter jets briefly entered Japanese airspace near the northern island of Hokkaido on Thursday.
The foreign ministry says the one-minute intrusion caused Japan's air force to scramble fighter jets in response.
Tokyo lodged a protest with Moscow over the incident, which it says was the first such intrusion in five years.
A Russian defense ministry spokesperson later denied that the jets had entered Japan's airspace.
The incident came after Japanese Prime Minister Shinzo Abe pledged to resolve a 60-year feud with Russia over northern territories.