JOIN USA Japanese media report said the drills were temporarily halted as a result on Monday, but Moscow said "Russia did not commit any breaches of international rules on the use of airspace or of flight rules".
The United States and Japan have been conducting their biggest ever joint exercise, which comes after regional tensions spiked following North Korea's deadly artillery strike against the South two weeks ago.
The two Russian Il-38 patrol planes on Monday flew over the Sea of Japan, where the drill was taking place, Japan's top government spokesman Yoshito Sengoku said, confirming a report in the Sankei Shimbun daily.
Sengoku, the chief cabinet secretary, told a news conference that Japan immediately dispatched fighter jets to the area off the Noto Peninsula in central Japan but he gave no further details.
A spokesman for Russia's Pacific Fleet, Roman Martov, told Interfax news agency: "The Il-38 planes mentioned in foreign media reports are serving in the Pacific fleet's marine aviation divisions.
"They were carrying out planned flights in the area of everyday activity for the fleet. Russia did not commit any breaches of international rules on the use of air space or of flight rules."
The massive US-Japanese "Keen Sword" war games include around 44,000 military personnel, 60 warships and 400 aircraft from both sides in a drill off Japan's southern islands, close to the South Korean coast.
The joint drills are larger than a naval exercise staged by Washington and Seoul last week, days after Pyongyang stunned the world with an artillery strike on a South Korean border island that killed four people.
Japan and Russia have quarrelled in recent months over a long-disputed island chain north of Japan's Hokkaido island which Soviet troops took in the final days of World War II.