A leading Soviet scientist said yesterday that any future deployment of military weapons in space, as contemplated by President Reagan's Strategic Defense Initiative (SDI), would end the prospect for further U.S.-Soviet cooperative space ventures. He said it also could make it difficult to solve international legal problems like the allocation of radio frequencies in space.

Roald Sagdeev, director of the Soviet Academy of Sciences' Institute of Space Research and one of Moscow's major spokesmen to the West on space matters, said at a public symposium that in his view it would be "absolutely incompatible" to expect cooperation from Moscow on civilian space ventures if the United States put weapons in space.

In explaining how Reagan's so-called Star Wars program could have an effect on civilian uses of space, Sagdeev pointed out there already was a "need for special international procedures to control radio frequency allocations," and added, "it might be very difficult to reach legal procedures if we start implementing weapons in space."

Sagdeev's remarks, which came at a symposium on weapons in space sponsored by the American Academy of Arts and Sciences and the Planetary Society, expanded on similar warnings earlier this year in Moscow in closed meetings with visiting American scientists.

Another version was contained in a critical study of the Star Wars program by the Committee of Soviet Scientists for Peace Against Nuclear Threat. The Washington Post obtained an English-language version in Moscow last week and published its findings. Sagdeev is deputy chairman of that committee and was on the working group that produced the study.

The study, which had earlier been circulated among American academics specializing in U.S.-Soviet arms control matters, said deployment of American space defense weapons "will practically block Soviet-American cooperation in the peaceful uses of outer space."

In a dramatic gesture, astronomer Carl Sagan, another participant on the panel, called for the United States to substitute for the Star Wars program a joint program to put an American and a Russian on Mars by 2003..

Sagan drew a sharp contrast between the president's plan to introduce weapons in space and "an extraordinary venture -- the U.S. and Soviet Union doing something on behalf of mankind."

Robert S. Cooper, assistant secretary of defense and director of the Pentagon's Advanced Research Projects Agency, said scientists and others who want to describe "space as sanctuary" are "unrealistic and not helpful" in the current debate.

He said critics of Star Wars were focusing on something that "may happen in the future" and failing to pay attention to the increasing number of military support systems that the Soviet Union and the United States will be sending into space in the next 10 years.

Cooper added that the president's program would benefit the civilian space program and would not take funds away from it.

"The impacts on the civil space program from the military," he said, "will be minimal."

Lt. Gen. James A. Abrahamson, director of the SDI program for the Pentagon, sent a strong speech in support of the civilian benefits of the program to the meeting. Speaking in Abrahamson's place, Greg Canavan, a physicist from the Los Alamos National Laboratory, declared that SDI would "enhance" the civilian space program and "might so stimulate the national economy that it will pay for itself."

At the same time, however, Canavan said successful deployment of space weapons could depend on the cooperation of the Soviets and other nations capable of sending objects into space. He said that international rules setting aside "an exclusion zone" for such weapons would be needed, much as rules exist today setting areas aside for military ships and military aircraft.

The need for Soviet cooperation in space radio frequencies during the U.S. space probe to Jupiter was pointed out during yesterday's session by Bruce Murray, former director of the Jet Propulsion Laboratory that ran the program.

At that time, Murray said, a Soviet military satellite was transmitting from space on a radio frequency that interfered with the weak signal coming from the U.S. space vehicle.

"In advance," Murray said, "it was arranged to turn that satellite off," thereby enabling the U.S. signal to come through.

The space program, he added, "only operates by good will" between nations with space programs.

In a television interview yesterday, Defense Secretary Caspar W. Weinberger said that funding of Star Wars and the MX intercontinental ballistic missile program was "absolutely essential" to success in the future arms control talks.