In an unusual move, the Senate Foreign Relations Committee voted 14 to 3 yesterday against a U.S.-Japanese nuclear agreement that lawmakers charged would authorize regular air shipments of hazardous plutonium across Alaska and possibly other areas of the United States.

Led by Sen. Alan Cranston (D-Calif.), the committee voted to return the pact to President Reagan, and asked that it be renegotiated or brought to Congress under a stricter law.

Cranston charged that the agreement would allow shipment of several hundred pounds of plutonium, an extremely potent cancer-causing agent, to Japan in the next 30 years in casks "not yet invented."

The committee action was intended to "stop the clock" on the 90-day period during which Congress is allowed to block executive agreements. The size of the committee vote and its composition, which includes Sen. Jesse Helms (R-N.C.) and most other committee Republicans, suggested that the full Senate will vote against the agreement unless major changes are made.

Ambassador-at-large Richard T. Kennedy, chief U.S. negotiator of the pact, testified that it provides "the most sweeping enhancement of U.S. controls over a foreign nuclear program in history."

He added that the radioactive plutonium may be shipped by sea rather than air.

The plutonium is produced for Japan in France and Britain from spent uranium fuel originally supplied to Japan by the United States. The fuel's U.S. origin gives the United States control over its later uses. The accord suggests a polar route so that the plutonium, raw material for nuclear weapons, will not transit likely areas of civil disorders or instability.