With Sen. John W. Warner (R-Va.) not voting, the Senate Armed Services Committee in closed session yesterday rejected on a 9-to-9 vote the Navy's plan to disperse its fleet around the United States rather than concentrate its ships in a few ports, notably Norfolk.

Warner voted against the dispersal proposal when it came before the military construction subcommittee but was under pressure from fellow senators and Navy leaders to go along with it yesterday. Last night an aide said Warner had been called away on urgent business during the three 9-to-9 votes on the plan.

The homeporting issue, which is expected to be fought anew on the Senate floor when the fiscal 1987 military construction bill is voted, turns on whether the strategic and political advantages the Navy says would be gained from homeporting is worth the cost of dispersing the fleet. Lawmakers from states where ships would be based have lobbied heavily for approval of the Navy plan.

The Navy estimates it would cost about $283 million more to build new ports than to renovate existing ones, and that the annual operational cost would run an additional $35 million to $50 million. The committee staff estimates that dispersal would cost an additional $540 million in construction and up to $300 million more annually for supporting the men and ships.

Under the Navy plan, ships would be homeported in Staten Island, N.Y.; Everett, Wash.; Lake Charles, La.; Pascagoula and Gulfport, Miss.; Galveston, and Corpus Christi, Tex.; Mobile, Ala., and Pensacola and Key West, Fla. Other ships would rotate among ports in Hawaii, San Francisco and Long Beach, Calif.

Last year the committee approved $89 million in construction funds for Staten Island and Everett but held up the money until the Navy had submitted a full report on the costs involved. Yesterday's vote keeps that money locked up.

Sen. Daniel Patrick Moynihan (D-N.Y.), whose state would benefit from the homeporting plan, called the vote an "aberration" to be corrected when the military construction bill reaches the Senate floor.

Eight Democrats joined Chairman Barry Goldwater (R-Ariz.) in voting against the plan, committee sources said, while Sen. John C. Stennis (D-Miss.) sided with eight Republicans in favor of dispersal.