Tokyo on Thursday expressed "extreme regret" after Moscow denied claims that a Russian military plane had violated Japanese airspace.
The alleged incident occurred last week when Japan claimed an IL-38 military plane violated the country's airspace three times off the coast of its northernmost island of Hokkaido.
Tokyo later filed a protest with Moscow over the issue.
However, Russian Foreign Ministry spokeswoman Maria Zakharova rejected Japan's claims, as well as the protest.
Zakharova said Moscow "could not confirm" the alleged breach reported over waters in the Sea of Japan on Sept. 23.
At a news conference in Tokyo, Japanese Chief Cabinet Secretary Yoshimasa Hayashi described Russia's denial as "extremely regrettable," Tokyo-based Kyodo News reported on Thursday.
Japan's claim came at a time when Russia and China were both holding large-scale military drills in the Pacific.
