TOKYO, DEC. 10 (THURSDAY) -- Japanese fighter jets fired shots yesterday to warn off a Soviet bomber flying over the Japanese island of Okinawa, where one of the largest U.S. bases is located.

Japanese fighters routinely intercept Soviet bombers that fly near or over Japanese airspace, but this was the first time since the end of World War II that Japanese aircraft have fired live ammunition at a Soviet plane, Japanese Defense Agency officials said yesterday.

According to agency officials, tracer bullets and ammunition were fired only after the Soviet Tu16 Badger bomber failed to respond to less aggressive warnings by radio.

The Soviet plane flew over the Okinawan islands twice, for a total of about 10 minutes, before leaving Japanese airspace and heading west toward the East China Sea and then presumably toward the large Soviet base in Vladivostok, officials said.

Foreign Ministry officials here said it was unclear whether the Soviet aircraft action was intentional, but the government will lodge a formal complaint with the Soviets.

"We don't understand what the meaning of this is intended to be," said one Foreign Ministry official, who spoke on the condition that his name not be used. He said that with the signing in Washington on Tuesday of the U.S.-Soviet treaty to scrap intermediate-range nuclear missiles, "I don't think this is a military demonstration."

One official suggested the Soviet plane may have been part of a reconnaissance effort to observe joint U.S.-Japanese air maneuvers that ended yesterday in Okinawa. The Tu16 had been flying in formation with three other bombers, but the others did not fly over Japanese land.

Soviet long-range aircraft often fly close to Japan on routes between the Soviet base at Cam Ranh Bay in Vietnam and the one in Vladivostock, officials said. According to Pentagon officials, the Soviet planes often conduct mock attacks near Japan, getting in position to launch missiles toward Japanese cities.

Most of the 20 Soviet incursions into Japanese airspace have occurred only over Japanese seas. In only three other cases have Soviet aircraft flown over Japanese land.

The most recent of these occurred in August, when a Soviet bomber flew over Hokkaido, Japan's northernmost island. The Japanese lodged a formal protest then, and Moscow eventually apologized.

In none of the other three cases did the Japanese have enough time to scramble fighters to confront the Soviet planes.

Japanese fighters were scrambled 825 times in 1986 to respond to suspected Soviet aircraft, military officials said. Fighters are on 24-hour standby at the major air bases, they added.

According to defense officials, yesterday's incident began when Japanese radar at Naha, Okinawa, spotted an unidentified aircraft heading toward the island and scrambled two Japanese F4 Phantoms from the Naha Air Base.

The Japanese fighters first warned the Soviet pilot by radio that he was approaching Japanese airspace. When they received no response, they wagged their wings and flew near enough to the Soviet aircraft to signal the pilot to land his plane at Naha, officials said.

When they still received no response, the Japanese fighter fired a warning burst of tracer bullets and ammunition. The Soviet plane stayed inside Japanese airspace until several more warning shots were fired, officials said.

Officials also said the Japanese pilots fired several bursts from a multibarrel 20-mm cannon that could have shot down the Soviet plane if the bullets had hit it. The shots were not fired at the front of the Soviet bomber, officials said.

"Usually when a Japanese pilot gives a correction to a Soviet pilot, they follow it," said Capt. Ken Hibino, an agency spokesman. "But this time was different."