The Air Force yesterday dealt another blow to Fairchild Industries Inc.'s bid to keep its T46A trainer alive by refusing to reinstate the aircraft in its budget.

In February, the Reagan administration had called for canceling the $3.5 billion jet trainer program in its proposed fiscal 1987 budget because of budget constraints.

The Chantilly, Va., company had hoped to reach a compromise with the Air Force by selling it 11 trainers for $105 million, down from 44 trainers that would have cost $350 million in fiscal 1987. The tactic evidently fell short of convincing Air Force Secretary Russell Rourke to continue the program.

"Although the T46A has performed satisfactorily in the flight-test program, the schedule delays and manufacturing problems, coupled with lack of affordability, made this decision necessary," an Air Force spokesman said.

The Air Force says it also will withdraw $170 million appropriated in fiscal 1986 for 33 of the trainers. The Air Force is paying Fairchild Republic Co., the Long Island division that makes the trainer, for 10 of the craft plus two prototypes as part of 1985 appropriations.

William Fulwider, a spokesman for Fairchild, expressed disappointment with the decision. "We thought the Air Force would find a way to continue the program, possibly at a reduced procurement level, because of the critical need for the trainer," he said. "We believe there is strong support in Congress for continuing the program."

Company officials have said the plant would have to be closed if the trainer is not reinstated, putting hundreds of Long Island jobs on the line. But the fight for the trainer is far from over on Capitol Hill, where program cuts may not be decided until late this year.

Senate Majority Leader Robert J. Dole yesterday praised the Air Force decision as putting Cessna Corp.'s T37 "back in the hunt" and as a "savings to the taxpayer of billions of dollars." Cessna is based in Dole's home state of Kansas.

But Rep. Thomas Downey (D-N.Y.), whose district includes the Fairchild plant, said yesterday he is confident that the trainer would be restored to the budget. "This means that Bob Dole wins this round, but, frankly, I think we'll win the next round," he said.

Fairchild said it has ironed out T46A problems. The Defense Department recently left the trainer out of the budget after an Air Force inspection of the Long Island plant turned up technical problems in the jet and "sloppy management."

The Air Force said its options now would be to modify 25-year-old Cessna T37 trainers, find another company to build the T46 using Fairchild's specifications, redesign a trainer from scratch or see what else is immediately available.