After years of urging Moscow and Washington to reach an accommodation to limit missiles in Europe, several allied governments are having second thoughts about getting rid of the controversial weapons that once triggered massive public protests and the collapse of previous arms talks when deployment began in late 1983.

The West European allies have expressed concern that removing all U.S.-built cruise and Pershing II missiles from their territory as part of a possible arms accord with the Soviet Union could undermine American nuclear guarantees in Europe and aggravate the threat of Soviet advantages in conventional forces.

At the heart of the anxiety over the fate of the missiles is the so-called zero option, which calls for the cruises and Pershings to be scrapped if the Soviet Union dismantles its SS20 missiles aimed at Western Europe.

President Reagan and Soviet leader Mikhail Gorbachev have suggested recently that a separate agreement curtailing or eliminating medium-range missiles in Europe might become the first tangible agreement at the Geneva arms negotiations, with deals on space and strategic nuclear weapons to be worked out later.

Reagan originally offered to cancel deployment in Europe of the cruises and Pershings if the Soviets scrapped the SS20s. The proposal was initially embraced by the Europeans, then dismissed as too unrealistic to be negotiable.

Lately the zero option has been revived as part of Gorbachev's sweeping plan for global nuclear disarmament by the end of the century. The Kremlin leader proposed last month that the United States and the Soviet Union eliminate missiles in Europe.

But he attached two key conditions: Moscow would be allowed to keep 170 of the mobile SS20s now believed to be based in Asia, and France and Britain must agree to freeze their own nuclear forces, with the United States undertaking not to transfer any missiles to its allies.

The emerging U.S. counteroffer, designed to challenge Gorbachev's vision of drastic cuts in nuclear stockpiles, would accept the notion of banning all medium-range missiles in Europe only if Moscow cuts in half its Asian-based SS24 force and drops its demands for a freeze on French and British nuclear arsenals.

U.S. officials indicated that this position might be advanced formally as the Soviet Communist Party Congress opens Feb. 25, in an effort to steal some political thunder from Gorbachev, who is expected to use the forum to extol the importance of his own arms control offer.

The surge of interest in an agreement on missiles in Europe, particularly after Gorbachev confirmed that he would endorse an early deal distinct from the complex talks on strategic and space weapons, has inspired more caution than enthusiasm in European capitals.

At the same time, Japan has emphasized that any agreement on medium-range missiles in Europe must not come at the cost of raising the nuclear stakes in Asia.

During consultations at North Atlantic Treaty Organization headquarters in Brussels last week, Paul Nitze, the special presidential adviser on arms control, was informed by allied ambassadors about the consternation being stirred in their capitals by new signs of movement toward a deal on missiles in Europe.

Some allied officials fear that the strong political motivation to strike some kind of arms agreement with Moscow could impel the Reagan administration to accept an accord that would detach European security from that of the United States.

"The whole idea of bringing the missiles over here was to reinforce the nuclear link between Europe and the United States," a West German official said. "After all the agony and protests over deployment, we will probably go through a new debate now over how credible is the American nuclear umbrella."

Other experts noted that if Moscow halved its SS20 force in Asia as Reagan suggests, it would retain almost as many of the triple-warhead missiles as it had stationed throughout the country when NATO adopted its deployment strategy in 1979.

Moreover, Bonn would also like the United States to persuade the Soviet Union to reduce or get rid of short-range missiles, now based in East Germany and Czechoslovakia, that are not under discussion in Geneva but threaten West Germany just as much as the SS20s.

Foreign Minister Hans-Dietrich Genscher has warned that withdrawal of the cruise and Pershing missiles from Europe would leave West Germany more vulnerable to the numerically superior conventional forces of the Warsaw Pact. He and Chancellor Helmut Kohl have pleaded for parallel progress to be achieved in other negotiations involving nonnuclear matters, such as the East-West talks in Vienna on troop cuts in central Europe and the Stockholm conference to reduce the risks of accidental war.

In a speech to the Stockholm delegates last month, French Foreign Minister Roland Dumas said, "For us Europeans, the limitation of nuclear weapons cannot be considered sufficient. The heart of the problem is the question of security; it must be considered in all its elements. We cannot accept that the problem of conventional weapons should be given lower priority than nuclear negotiations."

British Prime Minister Margaret Thatcher's government also has echoed the French and West German view about an imbalance of forces if the missiles are removed.

"There's no doubt about it," a British official said. "A denuclear world, or even a world with substantial nuclear reduction, that is not accompanied by changes in Soviet conventional strength is not acceptable."

The zero option, as put forward by Reagan and Gorbachev, "leaves a gap in the spectrum of nuclear deterrents," another British official said. "There have always been subliminal reservations among our military people about zero option."

Despite frequent assurances by the United States that it would never negotiate about the nuclear weapons possessed by sovereign allies, Britain and France are becoming increasingly concerned that they will soon experience intense pressure to sacrifice their plans to modernize nuclear deterrent forces for the sake of the first arms control accord between Washington and Moscow in many years.

During the next decade, Britain intends to replace its aging Polaris fleet with four new submarines purchased from the United States. Each submarine will carry 16 Trident II missiles packing eight warheads apiece that can be aimed at separate targets. France also has begun to install multiple warhead missiles on its submarines, so that by the end of the 1990s nuclear arsenals of both countries will grow to more than 1,000 warheads.