Japan has accused Russia of violating its airspace over the Pacific Izu islands and demanded an explanation.
Japan said the aircraft had violated its airspace for about three minutes
A Russian Tupolev 95 bomber flew for about three minutes over the isle of Sofugan, 650km (400 miles) south of Tokyo, Japanese officials said.
Japan responded by scrambling 22 jets and lodging an official protest with the Russian embassy.
But a spokesman for the Russian air force denied any incursion into Japanese airspace had occurred.
Alexander Drobyshevsky told Russia's Itar-Tass news agency that strategic bomber flights had been "carried out in strict accordance with international rules on flying over neutral waters, without violating the border between the two countries".
Russia last violated Japan's airspace in January 2006 near Rebun Island near the northern island of Hokkaido, Japanese officials said.
On Thursday, Japan held an annual rally to demand the return of four disputed islands - known as the Kurils in Russia and the Northern Territories in Japan - which Russia seized in the closing days of World War II.
The dispute has prevented the two countries from signing a peace treaty to formally end the war.
It was not clear whether Saturday's flyby was related to the rally.
Despite their territorial disputes, Japan and Russia have recently indicated their desire to improve relations, the BBC's Chris Hogg reports from Tokyo.
Russia wants Japanese financial support for development of its far eastern regions while Japan wants greater access to Russia's oil reserves.
Whether the alleged incident was a mistake or something more sinister, such as an attempt to test Japan's defensive tactics, it has rattled the Japanese government, our correspondent says.
Tokyo has demanded a full explanation from Moscow.