The first phase of a "Star Wars" missile defense system cannot be deployed before the turn of the century and will cost more than $170 billion, figures that contrast sharply with more optimistic administration estimates, a new congressional study has concluded.

Even if the system worked as planned, it would intercept no more than 16 percent of incoming Soviet missiles and would be capable of defending only a limited number of missile silos and military installations, leaving American cities wholly unprotected, the report from three Democratic senators claims.The space-based missile defense system "is embarked on a schedule it cannot achieve, with assumptions of funding that will not be forthcoming," the report warns. "When coupled with significant underestimates of Soviet responses, this is a prescription for financial and military disaster."

The Pentagon, in a written response to the study, said it contains "more misleading assertions than facts."

The Pentagon's strategic defense office disputed the report's contention that "Star Wars" would stop only 16 percent of Soviet missiles but said that the actual figure is classified. It also said that the first part of the program will cost no more than $150 billion and will be ready for deployment "at the earliest possible moment." It was not more specific about the program's timetable.

The Pentagon office, which is responsible for the "Star Wars" program, also said that both military and civilian targets would be protected by the space shield.

The Senate report, drafted by aides to Democratic Sens. J. Bennett Johnston of Louisiana, Dale L. Bumpers of Arkansas and William Proxmire of Wisconsin, is the latest of several studies raising doubts about the viability of the missile defense program.

A study released last month by the Pentagon's Defense Science Board urged that the program, formally known as the Strategic Defense Initiative, be broken into smaller, more realistic stages, beginning with a limited, ground-based system of rocket interceptors.

The report said that "technical, budgetary, political and arms-control uncertainties" surrounding "Star Wars" were likely to slow or halt development of a broad defensive system.

In another study, House Democrats found that the Strategic Defense Initiative was unlikely ever to meet President Reagan's goal of making nuclear weapons obsolete and warned that the Soviets could develop cheap and effective responses to any American "Star Wars" program.

And last week, Congress' Office of Technology Assessment, after a two-year Strategic Defense Initiative study, found that the defensive system was likely to suffer "catastrophic failure" the first - and presumably only - time it was used because of flaws in computer software. The Office of Technology Assessment report also concluded that the Soviets could easily counter the missile shield with anti-satellite weapons, leading to a destructive arms race in space.