MOSCOW, JUNE 16 -- The Soviet Union warned today that it might keep some of its shorter-range nuclear-armed missiles in Eastern Europe if West Germany insists on maintaining similar missiles on its territory.

Foreign Ministry spokesman Gennadi Gerasimov said at a press briefing today that U.S. insistence that West Germany's Pershing IA missiles fall outside the realm of negotiations in Geneva would "circumvent a Soviet-American accord and deprive it of real substance."

The dispute involves 72 West German missiles, equipped with nuclear warheads that are under American control. Washington and Bonn have said that the 72 Pershing IA missiles in West Germany are "third-country" weapons and therefore are not subject to U.S.-Soviet negotiations in Geneva.

The Soviet Union has argued that since the nuclear warheads are under U.S. control, they should not be considered separately from a U.S.-Soviet agreement being negotiated to eliminate medium-range nuclear missiles in Europe.

"If today, the United States received the right to set aside warheads for the West German shorter-range missiles on a legitimate basis, as it were, tomorrow it might well wish to carry through the same operation in Italy, Holland, Turkey or other NATO countries," Gerasimov said.

"Theoretically speaking, one can imagine a situation whereby the Soviet Union's allies in the Warsaw treaty could ask the Soviet Union to keep on their territory SS12 shorter-range missiles and provide them with Soviet nuclear warheads," Gerasimov said.

One western diplomat stressed the hypothetical nature of Gerasimov's warning, saying the Soviets are unlikely to give their allies control over the SS12 missiles.

According to published U.S. estimates, the Soviet Union deployed 65 SS12s in East Germany and Czechoslovakia as part of its response to the deployment of NATO's Pershing II and cruise missiles in 1984. Under the terms of a Soviet proposal now under negotiation in Geneva, the SS12s, which have a range of 560 miles, as well as other shorter-range and medium-range nuclear weapons in Europe would be dismantled.

{In Geneva, the United States formally proposed Tuesday the global elimination of shorter-range intermediate nuclear forces, The Associated Press reported. President Reagan announced the initiative Monday night.}

Gerasimov today noted that Bonn has pledged under the nuclear nonproliferation treaty not to deploy nuclear weapons. Since the United States is the owner of the Pershing IA warheads and retains control over them, "such warheads can in no way be considered 'armaments belonging to third countries' and hence should be in the number of American warheads slated for elimination," he said.

He said the NATO position on the Pershing IAs "will in no way promote the accomplishment of the task of elimination in Europe of the entire complex of medium-range and shorter-range missiles."