If a Japanese submarine rammed an American freighter, there would be a rapid pinpointing of institutional blame in Tokyo. Within a few days a high official -- probably the head of the Japanese Defense Agency -- would resign.

But in the United States responsibility is individual, not institutional, and the fixing of liability requires lengthy proceedings. So a fortnight after the nuclear sub George Washington sank a Japanese freighter, and then submerged, leaving two Japanese crewmen to die, the Pentagon is still investigating. Naturally, the Japanese are furious.

The deep cultural conflict implicit in the handling of the submarine incident is now becoming increasingly explicit as a factor in international politics. It figures in the difficult negotiations over limiting Japanese auto exports to the United States. It enters into the bickering about the Japanese defense program. It finds general expression in confusion as to the role Japan should play in the world at large.

In the auto negotiations, the Japanese have a strong interest in voluntarily cutting back exports below the level of about 1.9 million cars reached in 1980. Unless there is voluntary restraint, Congress is apt to pass tight quotas extending over a long period of time. Any action the United States took against Japanese exports would be more than matched by the countries of Western Europe.

But Japanese auto makers are reluctant to accept voluntary limits at this time because they see the possibility of a few good years in the American market. Japanese political leaders are loath to fight the car manufacturers unless pushed by the United States. So they have been visiting Washington in droves, looking for directions as to what the United States wants.

The Reagan administration has not flashed clear signals. In keeping with his free enterprise ideology, the president has said of autos that "I believe in free trade." Behind the scenes, though, he has instructed American officials to press the Japanese for a voluntary limit of about 1.5 million cars annually for a three-year period.

That double talk has exacerbated the troubles for the government of Prime Minister Zenko Suzuki. It now looks as though the best the prime minister will be able to get before he visits this country on May 7 is a loose, one-year commitment to a level of about 1.7 million cars.

As to the defense program, World War II gave many Japanese a bellyful of militarism, and the denouement at Hiroshima implanted in Japan an allergy to all things nuclear. The Japanese constitution formally "renounces war" as an instrument for settling international disputes. Government policy prohibits the deployment, transport or storage of nuclear weapons on Japanese soil or in Japanese waters.

Washington has been highly respectful of Japanese sensitivities in military matters. The United States keeps Japan in the dark as to nuclear deployments. This country has been slow to press the Japanese for a defense buildup.

Emergence of the Persian Gulf as the vortex of world politics changed that. Americans forces were strained, and the United States invited the Japanese to take up the burden. The Carter administration sought much larger efforts at sea and in the air. The Reagan administration has asked for a bigger effort in ground forces.

So far, the Japanese response has been disappointing. A pledged increase in defense expenditures by 9 percent in 1981 was watered down. The submarine incident has unleashed a spate of suspicion regarding the reliability of American support. A Socialist deputy, Yusaka Yayama, asked, just after the sinking, how, "if it was possible to save lives" then, one could talk ". . . of the U.S. maintaining security" for all of Japan in the future.

Ideally, these differences should be engrossed in a larger accord as to respective roles in the world. But the Japanese want to maintain their present posture as an economic giant without broad military and political responsibilities. The United States, while prepared to ask the Japanese to share specific burdens, has never figured out a large international task worthy of Japan's special genius and high capacity.

Perhaps the best that can be done in these conditions is to acknowledge the conflict in cultures. The United States can make a larger effort to give Japan the clear signals that are so dear to a nation with a strong capacity for developing consensus under the spur of necessity.

But even so, two economic giants of the non-communist world will probably have to bump along, devising joint approaches to particular problems, and hoping to hold differences to a minimum.