WASHINGTON (AP) _ Soviet President Mikhail S. Gorbachev's toughened stance on submarine- launche d cruise missiles could delay completion of a strategic weapons treaty past the summit planned for June, says a senior U.S. official.

Gorbachev and his foreign minister, Eduard A. Shevardnadze, appeared at the Malta summit last weekend to ''walk back'' from a concession they made in September concerning the submarine-launched cruise missiles, or SLCMs, said a second official. Both sources spoke on condition of anonymity.

At a September meeting in Wyoming with Secretary of State James A. Baker III, Shevardnadze withdrew Soviet demands that SLCM limits be included in the proposed Strategic Arms Reduction Treaty. Shevardnadze said the Soviets would settle for a separate deal, but did not specify whether it must be signed at the same time as the START treaty.

At Malta, however, the Soviets spelled out new, more stringent conditions for the proposed SLCM accord, and they have been indicating that they want the two deals concluded simultaneously, said the sources.

''In September, they said SLCMs could be dealt with outside the START treaty. But Gorbachev said 'how can we agree to all these kinds of reductions when SLCMs are out there running free?''' said the official.

Gorbachev also pressed President Bush to hold naval arms control talks to ban short-range nuclear weapons in the superpower navies, said White House spokesman Marlin Fitzwater.

Bush rejected Gorbachev's suggestion as ''unacceptable to us because the United States is a naval power. We depend upon the seas for contact with all of our allies and with other continents of the world,'' Fitzwater said.

Gorbachev concentrated on the issue of tactical nuclear weapons, while Shevardnadze dealt in greater detail with the SLCM question in a separate meeting with Baker, said one of the sources.

The senior U.S. official said that as a result of the conflicting signals from Wyoming and Malta: ''I don't know where we are. But SLCMs is a major issue.''

The new Soviet position helps explain the sudden pessimism of U.S. officials who went to Malta hoping to conclude START in time for the summit scheduled for the last two weeks of June in the United States, but left the Mediterranean saying it could take longer.

Both leaders said before the summit that a START deal was possible by September, and at Malta they announced that Baker would travel to the Soviet Union next month to continue work on the treaty, which would cut long-range superpower arsenals by 30 percent to 50 percent, to 6,000 warheads apiece.

So far, the Soviets have not put forward a comprehensive proposal linking SLCMs and tactical nuclear weapons, or spelling out the scope of the issues they want covered in naval arms control talks.

But at Malta, Shevardnadze told Baker the Soviets wanted the SLCM issue included in a naval arms control treaty, that they wanted tough verification rules and they wanted to curb conventional and nuclear warheads, said one source.

The Soviets have been pushing similar conditions at the START talks in Geneva, and also have given ''indications that they want START and a naval treaty at the same time. They didn't say that specifically at Malta,'' said the source.

One official described Shevardnadze's statements at Malta as a ''hardening of the Soviet position.'' Another called it a ''walk back.''

Gorbachev illustrated his concern over the American Navy by giving Bush a map of U.S. naval bases, deployments and maneuvers around the Soviet Union.

In rejecting Gorbachev's argument, Fitzwater said, Bush maintained that ''the Soviet Union is a land-based power. But the navy is crucial to us in terms of maintaining all of our commitments around the world, maintaining open sea lanes and commercial lanes around the world.''

In Pentagon and other assessments, the U.S. Navy is considered to be mightier than its Soviet counterpart, having for example more aircraft carriers.

At the joint presidential news conference concluding the summit, Bush and Gorbachev staked out their basic positions on naval arms control, although neither went into detail.

''The time has come when we should begin discussing naval forces,'' Gorbachev said.

Bush replied, ''I'm disinclined to think that this is an area where we will have immediate progress.''