Sen. John W. Warner (R-Va.) said yesterday that he has once again scuttled the Navy's long-held plans to transfer more than 16,000 of its workers from Arlington to the Washington Navy Yard.

A Senate Armed Services Committee report to be issued Tuesday will bar the service from moving the civilian and military employes from Crystal City to the District during the next 10 years, Warner said.

The Republican senator, a member of the committee, said he had inserted the prohibition in a report on the fiscal 1984 military authorization bill this week. His action came after the House approved a report from its appropriations committee directing the Navy to accelerate its planning for the controversial move.

The House's action indicated it has accepted the Navy's arguments that consolidation of the service's offices at the 60-acre Navy Yard on the Anacostia could save millions of dollars in annual rents the federal government must pay for 11 leased office buildings in Crystal City. The Navy acquiesced last year to pressure from Virginia's congressional delegation and did not seek funding needed to begin what it has said would be a $200 million construction and renovation project at the yard in Southeast Washington.

"It's just impractical to carry out this idea," Warner said yesterday. "When you consider the enormous deficit we face, every effort must be directed to ensure that every dollar spent for defense is necessary and wisely used."

Warner's committee move seeks to halt the Navy from spending monies on studies, design and construction work. Warner aides said they believe that actions by authorizing committees, such as the Armed Services panel, should take precedence over actions by the appropriations committees when it comes to deciding where money should be spent.

"It is clear from the economic analysis prepared by the Navy in 1981 . . . that economics favor retaining existing leased space," Warner said the new Senate report will state. "With the current upturn in the economy and the consequent highly competitive environment in the real estate industry, it is expected that leasing options will be even more attractive in the future."

Irene B. Forde, Warner's news secretary, said the senator worked with Rep. Frank R. Wolf (R-Va.) and Sen. Paul S. Tribble (R-Va.) to draft the Senate provision. A House Appropriations committee staffer said that Wolf was "embarrassed greatly" last week by the fact that his staff had apparently not been alerted to the House Appropriations Committee report in June.

Janet Shaffron, a Wolf spokeswoman, said: "This is what we wanted to happen. We will continue to oppose any effort to move the Navy from Crystal City."

Warner's measure directs the Navy to report any new economic data that would "weigh in favor" of Navy Yard construction. The Navy had no comment.