President Reagan yesterday opened future federal employment to striking air traffic controllers, but made clear that he will never permit them to have the jobs they want most--their former positions in the Federal Aviation Administration's control towers.

Reagan's decision to remove the three-year bar to all federal employment for the 11,500 striking members of the Professional Air Traffic Controllers Organization (PATCO) fell far short of the demand by the AFL-CIO and other unions that the strikers be restored to their jobs.

PATCO spokeswoman Marcia Feldman called it "a cruel hoax" to offer federal employment in a time when federal agencies are cutting back personnel because of the Reagan economic program. "We're deeply disappointed," she said.

The president said he was acting out of compassion toward the strikers. "I am sure that many of those who were misled or badly advised regret their action and would welcome an opportunity to return to federal service," he said.

Transportation Secretary Drew Lewis said the action is "a final decision within this administration."

Lewis said that because of animosity between the controllers who struck and the roughly 2,000 controllers who crossed picket lines, it would be dangerous to let the strikers return to the towers.

"The morale at this point is high, and we believe that allowing the controllers who chose to strike to return to the FAA would be damaging to the safety and efficiency of our air traffic control system," Lewis said.

PATCO's Feldman said the union is asking Reps. William D. Ford (D-Mich.), chairman of the Post Office and Civil Service Committee, and Elliott Levitas (D-Ga.), chairman of the Public Works and Transportation subcommittee on investigations and oversight, to investigate whether the working controllers actually are alarmed at the prospect of the strikers' return.

Reagan indicated he would remove the federal service bar last week when he met with leaders of the Teamsters and the AFL-CIO.

"We are clearly disappointed," AFL-CIO spokesman Rex Hardesty said yesterday. "It is not what the AFL-CIO executive council had in mind last week when it asked the president to show compassion."

Air traffic around the nation was disrupted Aug. 3 when the controllers walked off their jobs. Reagan took a firm line, declaring the strike illegal because it violated the no-strike provision of their contract with the federal government. The strike was the first national walkout by federal employes.

Donald Devine, director of the Office of Personnel Management, said controllers who apply for federal jobs "will be treated the same as any other federal employe who left the federal service, with the exception that they will have to go through a new suitability determination."

This will test whether they were involved in any acts of violence or coercion in the strike.

Devine conceded that the Defense Department is the only government department with job openings in this era of government cutbacks.

The controllers will be eligible to apply for positions in the nation's military control towers--jobs Lewis said pay about half the $22,500 to $49,800 they earned with the FAA.

The FAA borrowed military controllers after the strike began.

About 75 percent of scheduled flights are now operating.