BONN, JUNE 1 -- West Germany's governing coalition today reluctantly accepted, with one potentially important condition, a Soviet offer to bar from Europe an entire class of short-range, superpower nuclear missiles as part of a planned deal also to eliminate medium-range missiles from the continent.

The decision removed a major obstacle to a U.S.-Soviet treaty to slash European-based missile forces. It was announced after a meeting of Cabinet ministers and leaders of the three parties in Chancellor Helmut Kohl's alliance.

This brought the Bonn government into line with the United States and the other NATO allies, which already have informally endorsed the main provisions of Moscow's offer, and ended a bitter, six-week debate within Kohl's center-right coalition.

But the government's action left many conservatives disgruntled. They said their legitimate objections to the deal had been swept aside because of President Reagan's desire to achieve a disarmament deal before the end of his term, and Prime Minister Margaret Thatcher's wish to be seen as a supporter of arms control during the current British election campaign, according to governmental and political sources.

The governing coalition issued a statement accepting the so-called "double-zero option." It provides for removal from Europe of short-range missiles, or those with ranges of between 300 and 600 miles, together with withdrawal of medium-range missiles in the 600-to-3,000-mile category.

The Bonn coalition attached only one potentially significant reservation to its acceptance of the "double-zero" proposal. It said that West Germany wanted to keep 72 Pershing IA missile systems, which are owned by the West German Air Force but whose nuclear warheads are controlled by the United States.

West Germany maintains that the Pershing IA missiles, like the nuclear arsenals of Britain and France, should be excluded from the bargain because the Geneva talks cover only U.S. and Soviet missiles.

That is in line with the current U.S. position at Geneva, but it pointed to a potential stumbling block. The aged Pershing IAs can travel about 450 miles and thus fall in the category of short-range missiles to be removed under the proposed deal, so Moscow has insisted that the U.S.-controlled warheads be withdrawn as part of the bargain.

West German political sources said, however, that there was a good chance that the Pershing IAs ultimately would be withdrawn despite Bonn's opposition. They suggested that the U.S. administration would not allow the Pershing IAs to stand in the way of a major disarmament accord.

"If the U.S. president decides to give them away, then we have to give them away. I believe we see very clearly that we may have no Pershing IAs by the end of this year," a knowledgeable conservative political source said.

The United States and the Soviet Union already have agreed on the broad outlines of the medium-range portion of the deal, but progress in the Geneva negotiations has been delayed by Bonn's skepticism over the Soviet short-range proposal.

The decision represented a significant victory for the detente-oriented policies of Foreign Minister Hans-Dietrich Genscher, whose small Free Democratic Party favored the "double-zero" package. Genscher maintained that Bonn should not stand in the way of a major disarmament agreement, especially when Washington supported it.

Conservatives in Kohl's Christian Democratic Union and its Bavarian-based sister party, the Christian Social Union, contended instead that the proposed deal would leave West Germany especially vulnerable to the Warsaw Pact's advantages in missiles with ranges of less than 300 miles and in conventional infantry and armored forces.

This "steel helmet faction" also argued that eliminating two classes of nuclear missiles at once was too large a step toward surrendering European-based nuclear forces needed to deter a Soviet attack. It maintained that the plan called for removal of U.S. missiles needed as a symbol of Washington's commitment to defend Western Europe.

"The whole thing naturally means a decoupling of America from Europe," said Franz Josef Strauss, leader of the Christian Social Union, as he left today's meeting.

"I belong to the 'regrettably' people," he said, referring to those who accepted the deal with reluctance.

Kohl planned to present Bonn's position formally on Thursday in a speech to the lower legislative house, officials said.

The Bonn coalition also recommended that negotiations on the short-range missiles should be considered "in connection" with efforts to achieve a balance in conventional and chemical weapons forces in Europe. That reflected a concession to the conservatives. But the coalition did not demand a link between the short-range and conventional issues. A demand, rather than just a recommendation, for such a link would have made a U.S.-Soviet agreement substantially more difficult.

Finally, the coalition urged negotiations aimed at reducing battlefield missiles in the range below 300 miles. But, here, too, it did not demand such talks as a condition for accepting the Soviet offer on missiles in the 300-to-600-mile range.

The United States, without applying public pressure, had urged the West Germans to make up their minds on the short-range issue before the Venice summit of seven leading western industrialized nations, which begins Monday.

The United States also made clear its preference for the "double-zero" option, although it said that it would support any decision reached by its European allies. Washington argued that there would be plenty of U.S. nuclear weapons in the European theater -- for delivery by airplanes, submarines, missiles and artillery in the under-300-mile range -- to deter the Soviets.

The conservatives, nevertheless, had hoped to forge a European consensus against the Soviet offer. In April, they believed that they had support from Britain and France for a plan for both the Soviets and Americans to have 80 missiles in Europe in the 300-to-600-mile category.

The turning point in the debate came when the British government announced on May 14 that it supported the "double-zero" proposal, Christian Democratic sources said. "After the British declaration, there was no chance to change opinions within NATO and within the government," a Christian Democratic Party official said.

The conservatives suffered another major setback when Genscher's Free Democrats scored major gains in state elections in Rhineland-Palatinate and Hamburg on May 17, with the missiles an issue.