Japan is struggling with a new kind of United States protectionism. In this case the issue is not trade but fishing rights and global protection of an endangered species.
The matter is rapidly developing into a politically hot issue both in Tokyo, where fishing rights are vital to the national economy, and in Washington, where environmentalists are suing the Reagan administration for being too soft on Japan.
Focus of the dispute is an international moratorium on commercial whaling set to take effect in 1986. The International Whaling Commission (IWC), which agreed to the moratorium two years ago, with a ban to begin this fall on sperm-whale hunting as a first step, has no enforcement power. Indeed, Japan legally exempted itself from the rule by filing a formal objection.
But a five-year-old US law sponsored by Sen. Bob Packwood (R) of Oregon and former Sen. Warren Magnuson (D) of Washington presents Japan with a tough choice. The US law subjects any country that ''diminishes the effectiveness'' of any international whaling conservation measure to a 50 percent cut in the allocation of fish it can take from US coastal waters. Essentially, Tokyo must choose between continuing to fish for whales in any waters or accepting a sharp cut in its annual Alaskan pollack catch off the US Pacific Coast.
Economically, it is a fairly clear choice. Japan nets about 10 percent, $500 million worth, of its annual fish take from US Pacific waters. Whaling by contrast is a $54 million annual business and a source of less than 1 percent of the country's protein supply, according to Yasu Kawamura, a spokesman for the Japanese Embassy here. But whaling for Japan is also bound up in national pride and tradition. It is viewed by many Japanese as a right no one can ask them to give up. In recent days Japanese fishery officials have been labeling US demands ''outrageous'' and ''unfair.''
''It's become a terribly sensitive issue,''concedes a US State Department official. In an obvious effort to try to keep the already strained US-Japanese trade relationship on a more even diplomatic keel, the US Commerce Department recently spent two weeks negotiating with a visiting Japanese fishery delegation here. In announcing the resulting compromise, administration officials said the Japanese would be allowed without sanctions to catch a limited number of sperm whales - 400 - both this season and next in exchange for withdrawing their objection to the IWC sperm-whale ban. US officials also said the Japanese would withdraw their formal objection to the 1986 moratorium by next April.
That announcement infuriated both the Japanese government, which insists that it has agreed so far only to the sperm-whale compromise, and American environmentalists, who say the US sanctions are mandatory and the federal government has no business making any such compromise.
''The situation is pretty simple really; it's the speculation that's made it complex,'' says Japanese spokesman Kawamura. He says the visiting fisheries delegation from Tokyo had a mandate to discuss the sperm-whale ban but not the larger moratorium issue, which the US ''suddenly'' raised in the course of the talks. Of the moratorium, he says: ''We haven't agreed on any point - it's not a fact.''
The US, backtracking slightly, now agrees that, technically, Japan has until April to decide on the moratorium. ''The decision is left to the Japanese but the consequences are crystal clear,'' says Dr. Dean Swanson of the National Oceanic and Atmospheric Administration, who was involved in the negotiations.
''What the US did was a craven sellout for political expediency without any consideration of the long-term consequences,'' insists Craig Van Note, vice-president of Monitor Consortium, a group of nine conservation and animal-welfare groups currently suing Secretary of Commerce Malcolm Baldrige and Secretary of State George Shultz for failing to apply US sanctions.
Mr. Van Note says the illegal compromise is the result of a ''very heavy-handed power play'' by the Japanese and the State Department. It not only delays the ''confrontation'' until the next whaling season, he says, but it also sets a precedent by which other whaling nations could ask for similar concessions.
Just a few days ago his group sent a letter to Secretary Baldrige documenting current Japanese sperm-whale catches and giving him until Nov. 28 to apply sanctions. If the secretary does not respond, the consortium will file for an immediate injunction.
The Reagan administration insists the Packwood amendment was never intended to be automatic but was to give the secretary of commerce a powerful tool to penalize or provide incentives to countries not inclined to go along with the whaling ban.