Whales, which have quite enough problems, have now got caught in the angry waters of U.S.-Japan relations. But the persons protesting on the whales' behalf during last week's visit by Japan's prime minister have a grand cause.

The campaign to save the whales is a rare and refreshing example of intelligence in the service of something other than self-interest. That is one reason why it has progressed tremendously. Last summer the member nations of the International Whaling Commission, responding primarily to appeals to conscience from groups like Greenpeace and the Animal Welfare Institute, voted 25-7 for a five-year moratorium on commercial whaling, beginning in late 1985. (Subsistence whaling by Eskimos and other natives around the Arctic Sea would continue.) But the three nations that kill 90 percent of the whales--the Soviet Union, Norway and Japan--may not comply.

Cheap substitutes now exist for all whale products, and no nation's whaling industry could exist unsubsidized. Japan kills the most whales and buys almost all the oil and meat from other nations' whaling. Japan's compliance with the moratorium probably would end commercial whaling. Whale meat provides less than 1 percent of Japan's protein. Japan's whaling industry has shrunk from five fleets to one, but several thousand jobs are involved.

The IWC is toothless, but U.S. law is not. Nations in defiance of IWC rulings can be denied fishing rights within the U.S. 200-mile zone, and imports of their fish can be stopped. The value to Japan of the fishing and imports is at least 10 times the value of Japan's whaling industry. Congress favors sanctions if commercial whaling continues in 1986.

Japan's policy may seem another instance of that nation's bloody-mindedness, and of Oriental concern with saving face. But the disapproval of Western nations, and especially the United States, strikes Japan as Occidental hypocrisy. In the 1830s and 1840s, American whalers depleted stocks in the seas around Japan. When Commodore Perry's fleet arrived in Japan in 1852, he was seeking supply stations for American whalers. Japan notes that Americans only became fastidious about whaling when whale products were no longer needed for lamp oil and margarine.

But such point-scoring misses the point--two points, in fact. The campaign against whaling has two distinguishable motives, conservation and humanitarianism.

More than 300,000 whales have been killed in the decade since the United Nations called for a moratorium. Every species of whale except the small Minke is endangered. It may be too late to save the magnificent blue whale. (They can exceed 100 feet in length; a baby can gain two hundred pounds a day.) IWC quotas have been cut from around 50,000 in the early 1970s to 12,365 in 1983. Whaling is a dying industry; the question is whether it will be extinct before some species are.

Humanitarian concerns include, but go beyond, the refusal of Japan and others to abandon "cold" harpoons which, lacking explosives, cause a prolonged death agony. Japan opposes explosive harpoons because they damage some of the meat.

It probably is virtually impossible to kill humanely a creature that large. But even if the problem of pain could be solved, this problem would remain: there is something unseemly, something subversive of our own dignity, about killing such splendid creatures.

Whether whales, with their complex brains, really are, as some scientists say, "our neurological relations" is less important than this: whales have individual personalities, complex social behavior and remarkable memories and capacities for communication.

As I sit with pen poised over paper, I am struck by the oddness of cataloging reasons for abandoning the killing-- the cruel and utterly unnecessary killing--of such mysterious creatures, about which we have so much to learn. It is possible, and not exactly wrong, to give practical reasons why saving the whales will be useful. But there are times, and this is one, for rising above utilitarianism.

It is important to say that life is enhanced aesthetically by the knowledge that these sociable creatures are swimming--and singing--on the surface of the sea, and in the sunless depths below. Furthermore, mankind has dominion over the Earth, but mankind's unsteady, serpentine path toward finer sentiments can be measured, in part, by evolving standards of what constitutes civilized dominion over lower animals.

Surely it involves a conviction, more intuitive than reasoned, that Creation, and we as the responsible portion of it, are diminished by wanton behavior toward creatures that so stunningly exemplify the mysteriousness of the natural.