Soviet ships defied Japanese authorities today by towing a disabled nuclear submarine through Japan's territorial waters. Japanese Prime Minister Zenko Suzuki called it an "unfriendly act" and said a strong protest would be lodged with Moscow.

Japan's relations with the Soviets already are strained by the buildup of Soviet troops on disputed northern islands. The Foreign Ministry had ordered the submarine to stay clear of its 12-mile limit unless the Soviets could assure that the sub was neither leaking radioactive material nor carrying nuclear weapons.

Tests by specially equipped Japanese ships did not detect unusual amounts of radiation in the sub's wake. But the Japanese are extremely wary of all nuclear weaponry.

An hour after the submarine left Japanese waters, a Soviet diplomat delivered a brief note to the Foreign Ministry stating that the warship carried no nuclear weapons and its reactor posed no danger of leaks.

Foreign Ministry officials, who earlier said Tokyo planned to protest "violation" of Japan's territorial sea later said the protest referred only to "passage without permission" through the waters.

The officicals explained that the japanese government had yet to decide if the towing operation violated the sea limit.

The government was checking to see if the ship's passage through the waters was allowed under an international convention granting all countries the right to "inoffensive passage" through territorial waters.

A Soviet Embassy official initially had told the Foreign Ministry that there was no danger of a radiation leak and asked permission for the submarine to pass through a 20-mile-wide strait in the Ryukyu Island chain.

Japanese officials, evidently unsatisfied by the explanation, refused. A few hours later, however, the submarine and its escorting vessels, including a sub tender and a tanker, sailed through the channel between Okinoerabu and Yoron islands, ignoring warnings from a Japanese patrol boat.

A Japanese destroyer, several patrol boats, including one equipped with radiation detection gear, and a patrol plane watched the Soviet ships but took no action.

After reaching the East China Sea, the Soviet vessels set a northward course toward their home port at Viadivostok, more than 1,000 miles away.

The Japanese vessels are expected to trail the Soviet flotilla as it moves northward through the Tsushima Strait, an international waterway between South Korea and Japan.

The 6,000-ton submarine was crippled by a mysterious fire Thursday in international waters east of Okinawa, about 80 miles from the nearest land. Soviet radio transmissions intercepted by the Japanese said nine sailors were killed in the fire, giving rise to worries in Japan about possible radioactive contamination of the sea an air.