The Air Force has restricted its entire B1 bomber force from low-altitude, high-speed flights as a result of a Sept. 28 crash that killed three of six crewmen, officials said yesterday.

The new restrictions, which officials said were imposed for safety reasons, are a significant setback for the bomber's already troubled training program. The B1 bomber's primary mission is to penetrate enemy territory at low, terrain-hugging levels to avoid enemy radar on bombing raids. Training already had been restricted in recent months, because the Air Force has had problems with the bomber's terrain-following radar.

The new restrictions virtually insure that there will be no testing of the plane in the very area for which it was proposed and sold by the administration to Congress: its ability to fly bombing runs fast and low to avoid enemy radar.

Strategic Air Command spokesman Col. Larry Greer said the new restrictions would impede training programs, but that the crews would make up the lost training time later.

"We are forgoing it {training} in the interest of safety," Greer said.

A B1 bomber crashed on a Colorado training range in September after the crew radioed that a bird had been sucked into the engines. The engines burst into flames and three crewmen ejected safely. Three others were killed in the crash.

SAC first suspended low, high-speed flights only in areas with large populations of migratory birds, Greer said. But nine days after that restriction, SAC suspended all low-level, high-speed flights "pending the outcome of the accident report" on the September crash. Greer said it is uncertain when the report would be completed.

SAC also briefly suspended the entire force of bombers after the crash in order to inspect the ejection seats for safety problems. No problems were found, Greer said.

Greer said the new flight restrictions apply in "peace time only" and that the bombers would be flown at all levels in the event of war. Greer said a "low-level" flight is one with an altitude ranging from 200 to 800 feet.

The $28 billion B1 bomber program is one of the cornerstones of the Reagan administration's strategic buildup. There are 73 bombers in service; eventually there will be 100. But the bomber has been plagued by numerous problems.

The Air Force has said it is uncertain how long it will take to fix problems in the bomber's electronic countermeasures equipment, designed to help protect the plane from enemy attacks.