A program to modernize the Soviet Union's medium-range nuclear missiles has led Moscow for the first time to use its nuclear weapons and their warheads for political as well as military purposes, according to U.S. analysts.

Six years ago, the Soviet Union began replacing its aging SS4 and SS5 medium-range nuclear missiles aimed at targets in western Europe with new, more capable, SS20 missiles. NATO responded by approving the stationing of new American Pershing II and ground-launched cruise missiles in western Europe beginning this December.

The Soviets say that they will deploy more SS20s in reaction to the American deployment. In addition, they are threatening another basic policy change: moving a significant number of nuclear warheads for short-range systems from the Soviet Union into Warsaw Pact countries.

These steps are producing the same type of concern among the Soviet Union's Warsaw Pact allies that the United States has faced in western Europe over introduction of its nuclear weapons.

Meanwhile, Washington and Moscow are accusing each other of stepping up the arms race, and in negotiations in Geneva have been unable to agree on a formula to limit or eliminate these systems.

The SS20 is a mobile, solid-fueled missile that carries three warheads and has a range of more than 2,500 miles. It has been replacing some 700, 20-year-old, liquid-fueled SS4 and SS5 missiles, which are less accurate and slower to put on alert, and carry giant warheads.

The SS20s are considered "garrison mobile systems" by the Strategic Rocket Forces, the branch of the Soviet armed services that operates them. In peacetime, the missiles normally would be kept unarmed in garages, according to experts on Soviet military systems.

They are not designed "for surprise attack," according to an American analyst familiar with the system. Any "bolt from the blue" first strike, he said, would be carried out by Soviet SS19 ICBMs, which are kept on alert in hardened silos and can hit targets in either western Europe or the United States.

The SS20 role, he said, would start after a conventional war has begun but before nuclear weapons have been used. The SS20s would be armed, taken from their garages and moved to remote, predesignated sites, where they would be put on alert.

Under Soviet military planning, the job of the roughly 250 SS20s aimed at western Europe is to destroy NATO's nuclear systems "before they can be used," he added. The 750 warheads carried by those missiles would be aimed at Pershing and cruise-missile launchers, which under full deployment would total 222, and other targets such as air bases, submarine facilities and nuclear-warhead storage sites.

The 125 SS20s based in the central and eastern portions of the Soviet Union are aimed at similar targets in China, Japan and Korea.

The 375 SS20s represent a significant increase in Soviet military capability over the missiles they replaced. However, in the past two weeks, Soviet military officials have said that additional SS20s will be deployed if the initial basing of U.S. Pershing II and cruise missiles occurs as scheduled in Europe.

Some analysts say the Soviets have deployed at least twice as many SS20 warheads aimed at Europe as they would need. Thus, Moscow's decision to build more is looked on here as a political act, to add to the threat to western Europe and to give the Soviets bargaining chips in the Geneva arms negotiations.

Also, Moscow has been threatening to shift its policy on stationing nuclear warheads outside the Soviet Union, according to government experts here. In a series of public interviews, members of the Soviet general staff have declared that modern, short-range missiles will be deployed with their warheads in Warsaw Pact countries.

Traditionally, the Soviets have kept nuclear warheads for short-range systems inside their homeland, even though launchers that would fire them have been deployed for years with their forces in eastern Europe.

Experts say that within the last few years the Soviets have placed a few warheads in East Germany. But U.S. intelligence experts disagree over whether those forward-based warheads were more than a test and whether they are still there. Some specialists say that they believe those warheads may have been removed.

The threat to put these nuclear warheads into East Germany, Czechoslovakia and Hungary for artillery and short-range missiles represents a major break with the past, according to experts on Soviet military systems.

Not all analysts say they believe that the Soviets plan to take such a step. There is, for example, disagreement over whether recent statements by Soviet General Nikolai Chervov, head of the legal and treaty department of the general staff, that "tactical nuclear weapons" are stationed outside the Soviet Union refer to launchers alone or to warheads as well.

Keeping Soviet warheads inside the homeland, these analysts say, is part of Soviet military writings. Under Soviet war planning, longer-range systems, such as the SS20, would be the first ones used in nuclear conflict.

The Soviet short-range nuclear weapons would be used later, to attack smaller NATO battlefield weapons remaining after the SS20 attack. Warheads for these short-range systems would be held in the Soviet Union to protect them from a conventional NATO attack and to enable them to be delivered quickly by air to battlefields.

In addition, the Soviets have always been concerned about warheads being sabotaged if they were stored in Warsaw Pact countries.

"They have been more cautious than us," one former Pentagon official said last week, noting that U.S. warheads have been kept in Europe for almost 30 years.

Another sign of the Soviets' caution is in the way their warheads are protected.

Custody of nuclear warheads, inside and outside the Soviet Union, is entrusted to special uniformed units of the KGB, the state security organization. In wartime, they are supposed to turn them over to army and air force commanders only after getting clearance from civilian leaders in Moscow.

"At Russian nuclear storage sites," one expert on Soviet systems said last week, "there is special command and control equipment for the military and an exact parallel system for the KGB, whether it is radio, telephone land-lines or satellite." That way, he said, both branches have direct lines to Moscow.

The exceptions, he said, involve warheads on ICBMs on alert in silos and missiles already on submarines.

A Soviet transfer of additional warheads to eastern Europe would come at a time when the United States, at the urging of its NATO allies, is about to remove more than 1,000 short-range nuclear warheads from Europe.

East European leaders are no happier with the prospect of having Soviet warheads on their territory than were west European officials who have had to deal with American nuclear systems in their countries, according to State Department officials.

The nuclear buildup in Europe illustrates the arms race. Moving warheads into eastern Europe would be a response in part to the planned December deployment in western Europe of the first new, medium-range American missiles. The U.S. missiles, in turn, are described by Washington as a response to the introduction, begining in 1977, of the SS20s.

The Pershing IIs could hit targets in the Soviet Union within 10 minutes after launch. Soviet General Chervov said recently that the Soviets plan to deploy systems "which could strike targets in the United States within 10 minutes."

Because Chervov ruled out using Cuba as a site for such missiles, American experts expect that the Soviets would place them aboard submarines or ships traveling along the eastern seaboard of the United States, putting them within range of such major cities as Washington, New York and Boston.

U.S. analysts discount talk that the Soviets might place SS20 missiles in the northeastern portion of their country to be able to hit Alaska and Seattle within 10 minutes. The Soviets do not consider such targets as important as Moscow and other Soviet cities threatened by Pershing missiles, these analysts say, adding that the cold weather in the northeastern part of the Soviet Union is another reason to believe missiles won't be placed there.

Both countries refer to the other's missiles as first-strike weapons, yet neither keeps many on alert, ready to fire.

Under U.S. deployment plans, one-third of the Pershing II missiles will be on 24-hour alert with their warheads attached. The rest will be kept unarmed in garages on their launchers.

And the SS20s that go out of their bases on training missions "are not armed," according to one expert.