The Japanese government is "flagrantly subverting" international efforts to save whales by allowing Japanese corporations to conduct pirate whaling operations, nine conservation groups charged yesterday.

The groups told a Senate Commence committee hearing that the Taiyo Fishery Co. and its subsidiaries, operating through a web of dummy corporations, have set up whaling operations in Peru, Chile, Taiwan, Spain, Cyprus and South Africa exporting some 10,000 tons of whale meat a year to Japan.

The charges cames as Congress is considering legislation to allow the secretary of commerce to deny fishing permits in U.S. waters to any nation that supports pirate whaling or exceeds its internationally approved whale quotas.

The bill, sponsored by Sens. Warren Magnuson (D-Wash.) and Bob Packwood (R-Ore.), has passed the Senate and is awaiting House action. It could severely affect Japan, which conducts millions of dollars worth of fishing operations within the U.S. 200-mile limit.

Assistant Secretary of State Thomas Pickering told the committee that the United States has "expressed grave concern" to Japan and other countries involved in pirate whaling. He said the United States has "pressed" the Japanese government to prohibit imports of whale products from countries that have not ratified the international whaling treaty.

Japan is the major world market for whale meat, which was once a staple of Japanese diet but now accounts for only 1 percent of Japan's protein consumption. Alan Macnow of the Japan Fisheries Association said, however, that whale meat remains "an important protein source . . . Wahaling has been a tradition in Japan for 1,000 years."

Macnow acknowledged that pirate whaling is "a serious problem" and said the Japanese government has tried to stop whale product imports from pirate operations, "but it didn't work." He said the government will keep trying.

Macnow added "It's very unfair to pick on Japan" when European countries also import whale products and Norway has sold harpoons to pirate whaling operations.

But William Aron, a Commerce Department official, said, "We're picking on Japan because they are violating the Pelly amendment. The only country importing [whale] meat is Japan. They are importing meat taken from whales in excess of International Whaling Commission quotas."

The Pelly amendment, enacted in 1971, allows the President to cut off U.S. fish imports from any country that violates international whaling rules. It has not been enforced against Japan or the Soviet Union, generally considered the major violators, because to do so would leave many U.S. canneries without a product to process.

Craig Van Note, speaking on behalf of Monitor, Defenders of Wildlife, the Fund for Animals, the American Society for the Prevention of Cruelty to Animals and other groups, showed the committee a film of whaling aboard the Sierra, a factory ship previously registered in the Bahamas, then in Somalia and now flying a Cypriot flag.

The film showed the harpooning of humpback whales, an endangered species whose killing is prohibited by the Internation Whaling Commission. It also showed Japanese "production inspectors" working aboard the Sierra. The ship is owned by a dummy corporation in Lichtenstein and sells its catch to Taiyo Fishery Co., Van Note said.

Pickering said the State Department has confirmed reports that a Taiwanese whaling vessel purchased from Japan took 290 whales in 1976-77. The department is checking reports that four more Japanese whalers have been sols to Taiwan, which has no whaling tradition and only recently began whaling. Taiwan has refused to join the International Whaling Commission.