The Reagan administration has decided to take another important step toward ending its adherence to the unratified SALT II treaty by telling the Soviet Union that after this fall, the United States will refuse to discuss compliance with that agreement in the Geneva commission set up to monitor arms control pacts.

According to informed sources, this message is being delivered to the Soviets this week by retired Air Force general Richard H. Ellis, American representative to the Standing Consultative Commission (SCC) in Geneva, which is meeting at the Soviets' request to discuss President Reagan's May 27 announcement that the United States would no longer respect SALT II.

An informed source said yesterday that the initial session of this SCC meeting in Geneva had been confrontational, with the Soviet representative harshly attacking U.S. policy.

According to one source, Ellis has been instructed to tell the Soviets that because of Moscow's "past behavior" in allegedly violating the SALT II agreement, "the strategic weapons limitations of obsolete past agreements are no longer fitting subjects in the SCC."

Instead, Ellis was instructed to say, the U.S. representative at the SCC next year would limit his discussion to matters arising out of the 1972 Antiballistic Missile (ABM) Treaty and an informal agreement between the two countries involving nuclear accidents.

This negative signal in Geneva this week contrasts with generally positive noises emitted from the Reagan administration in recent weeks as part of a continuing campaign to revive superpower arms negotiations and arrange a new summit meeting before the end of this year.

This week administration envoys have been consulting with U.S. allies over a draft response to the latest arms proposals from Soviet leader Mikhail Gorbachev, and sources said yesterday they expected the reply to be sent to Moscow in the next few days.

Reagan's new SCC decision may disturb U.S. allies who recently have urged the president to reconsider his decision to abandon SALT II. Two weeks ago, French President Francois Mitterrand declared in Moscow that he had told both Reagan and Gorbachev that "when it comes to treaties, one should set out with the intention of consolidating what has been achieved, not destroying it."

British, West German and other NATO officials have given Washington the same message. In Congress, members of both houses have introduced resolutions and legislation to try to salvage SALT II.

On the other hand, administration officials contend that Gorbachev's latest -- and thus far most forthcoming -- arms control proposals were made after the May 27 decision on SALT II.

Since May 27 the president has given conflicting signals about what he meant, refusing several times to describe the 1979 treaty as "dead," and saying that before making any definitive decision he would give the Soviets further opportunity to mend their ways by changing practices the United States considers violations of SALT II. Though the United States plans to exceed SALT II limits by deploying a 131st B52 bomber carrying air-launched cruise missiles, it could fall back below this limits again next year by dismantling an old Poseidon submarine that is due to go out of service.

The SCC is a U.S.-Soviet body established in 1972 that meets twice yearly to discuss problems arising out of arms control agreements between the two nations.

The commission has long been a target of SALT II opponents in the Reagan administration. For example, in a memo on the eve of the Reagan-Gorbachev summit in Geneva last November, Defense Secretary Caspar W. Weinberger advised Reagan to end U.S. participation in the SCC.

The Soviet request in late June for the special SCC session contained a question about how Reagan's SALT II decision would affect SCC deliberations.

Receipt of the Soviet message set off what has become a standard conflict within the Reagan administration between the State and Defense Departments. Initially, the Pentagon and the White House wanted to reject the meeting because it seemed an attempt to generate propaganda over an issue -- the abandonment of SALT II -- that was seen as a negative for Reagan.

State Department officials thought rejection would increase criticism of the policy and that the meeting would offer an opportunity to prove that that the SCC and SALT II had continuing merit. They wanted Ellis empowered to work out a new count of strategic missiles and warheads on both sides, as had been done at earlier SCC meetings. Such a data base would be needed if the two sides made an interim agreement -- an option Reagan suggested on May 27 -- under which the United States would not build more ballistic missiles or warheads than the Soviets deploy.

State Department officials also wanted to use the SCC to continue notifying the Soviets of changes in the deployment of U.S. strategic weapons related to limits on those arms contained in SALT II.

Pentagon officials reversed themselves and favored the session because it offered an opportunity to end the ambiguity over Reagan's decision. They wanted Ellis to tell the Soviets that neither they nor the United States was any longer bound by SALT II. In the future, Ellis was to say, the United States would use the SCC only to discuss the 1972 ABM treaty issues.

State officials did not oppose the idea of ending the SCC role in handling compliance issues, but did ask that the data base and notification proceses be continued. But Reagan rejected that proposal, opting instead for the stiffer instructions Ellis took to Geneva this week.