The Soviet Union warned West German Chancellor Helmut Kohl today that his election triumph does not constitute an endorsement of plans to deploy new U.S. nuclear missiles.

The results of yesterday's West German elections are a serious setback for Moscow's political strategy for preventing the deployment of 572 Pershing II and cruise missiles in Western Europe. Kohl has endorsed the U.S. plan for deployment if no agreements are reached with the Soviets during the current arms control talks in Geneva.

The catastrophic defeat of the Social Democrats, who were more reluctant about the deployment and were supported openly by the Soviets, has weakened Moscow's position at the Geneva talks, according to diplomatic analysts here.

Initial Soviet commentaries displayed keen disappointment with the West German outcome. The Novosti Press Agency said the victory of Kohl's Christian-Democratic Union and its sister party, the Bavarian Christian Social Union, was likely "to lend vigor and energy to the Reagan administration, which is counting days to December" when the missile deployment is due to begin. It also has made the outcome of the Geneva talks "more problematical," it added.

Moscow television said Kohl's attitude toward the missile question would determine whether West Germany will become a new center of tensions in Europe. The commentator expressed the hope that Kohl's conservative government would approach this problem by keeping in mind "the national interests of the federal republic and common sense and prudence."

But the tone of the commentaries was harsh and appears to foreshadow a tough Soviet reaction in the coming weeks. The government news agency Tass said the missile deployment would "complicate all" contacts between Moscow and Bonn.

Novosti said that despite the conservative victory "there are numerous forces in the country" opposing the missile deployment. To ignore them, it added, could "exacerbate the domestic political situation in West Germany, which is already tense due to record high unemployment."

"The world public, which is opposing the arms race, will look on the ruling quarters of West Germany as one people who are aggravating the nuclear danger and who have forgotten the lessons of World War II," the agency said.

However, the commentaries reflected a realization here that the defeat of the Social Democrats represented a loss of a "European alternative" for Moscow in its dealings with the United States. One comment focused on this by suggesting that the forthcoming U.S. presidential campaign could produce "its own amendments" to the existing situation.

One Novosti commentary, sent to Western wire services, also suggested a broader Soviet approach to Western Europe, whose "responsible" leaders were urged to consider the "consequences of the qualitative change in the strategic situation" should the new U.S. missiles be deployed.

A Moscow television commentary attributed the defeat of the Social Democrats to their failure to take a clear stand against the missile deployment and mobilize the entire peace movement behind it. It also said that West Germans had been subjected to "psychological brainwashing" by the United States.

However, the Soviets may have been the victim of their own propaganda and assessments of the internal German situation. It is obvious that the Social Democrats failed to attract the votes of new and young voters, about 2.5 million of whom added to the electoral rolls this time.