President Carter, in a concession to nuclear weapons laboratories, and the Pentagon, has ordered U.S. negotiators to seek a three-year comprehensive nuclear test ban treaty rather than the five-year pact the United States had previously proposed.

Carter's decision was transmitted whithin the past two weeks to U.S. negotiators at Geneva, and by them to the Soviet and British teams working on the proposed three-nation pact, according to informed sources.

The Russians, who have expressed irritation at the slow pace of negotiatinns, are reported to have responded with bafflement at the latest U.S. switch in signals.

A shift in the Carter administration position had been rumored since early summer, when opposing forces within the executive branch began reacting to Carter's May 20 decision to propose a five-year, zero-yield test ban at Geneva.

The reaction was so strong from the directors of the nuclear weapons laboratories at Los Alamos, N.M., and Livermore, Calif., and from some elements of the U.S. military, that close observers believe the entire test ban treaty porposal was "up in the air."

Carter's recent decision-making included a determination to continue on the course of a comprehensive ban on nuclear test, underground as well as in the atmostphere, and a decision to seek 10 monitoring stations in each country as a means of verifying compliance with the treaty, according to the sources. The Soviet Union earlier had agreed in principle to the "black boxes" on Russian soil, a break through in verification, but the details remain to be settled.

The Soviets are reported to be prepared to go ahead with a test ban treaty of any duration. At the United Nations last week, Foreign Minister Andrei A. Gromyko declared that it is important to bring the negotiations to a successful conclusion, and charged that "for some reason or other our negotiating partners are stalling."

The United States has consistently conducted about twice as many test explosions as the Soviet Union throughout the nuclear era and is believed to be well ahead of the Russians in warhead technology. It is also far ahead, about $10,000 to the Soviets' 5,000 in the number of warhead in its strategic nuclear force.

Some authorities believe that a cessation of atomic testing, by limiting the constant improvement of weapons designs, would do more to curtail the arms race than the strategic arms limitation talks (SALT) treaty now under negotiation between Washington and Moscow.

The weapons design laboratories, whose operations would be affected by a temporary ban and sharply curtailed by a permanent ban, have asked for a commitment that testing will resume at the end of the proposed treaty unless a permanent international test ban arrangement has been reached. Official sources said yesterday they know of no such commitment by Carter.

The president evidently has rejected appeals from the laboratories and some Pentagon officials to allow tests well into the metagon range to check the reliability of the U.S. weapons stockpile during the duration of the treaty. Officials emphasized yesterday that Carter is still seeking a "comprehensive" treaty.

At the time of the May 20 decisions, there seemed to be a real possibility that the test ban treaty with the Soviet Union and Britain could be signed before the SALT treaty with Moscow.The White House, informed that the test ban might be even more controversial on Capitol Hill than SALT, revised its timetable so that the strategic arms treaty will come first.

Reduction of the duration of the test ban from five year to three appears to be another effort to make it more palatable to opponents. But a major bureaucratic and political battle is expected when a treaty is completed, nevertheless.