Transportation Secretary Drew Lewis said yesterday that at least 12,000 striking air traffic controllers have lost their jobs and will not be rehired "as long as the Reagan administration is in office."

"It's too late now," Lewis said about the controllers who defied presidential orders to go back to work on their first shifts after 11 a.m. Wednesday in their respective time zones.

"As far as we're concerned, this is no longer a strike situation. We're beginning to rebuild the system," Lewis said, speaking on the fourth day of a nationwide strike that has disrupted air service, cost the nation's airlines millions and set precedents for federal labor relations.

There were 17,200 controllers in the nation's air traffic control system when the strike began, and Lewis and Federal Aviation Administrator J. Lynn Helms said yesterday that they are prepared to cope with reduced staffing levels initially through measures that include:

Closing 58 air towers around the country that were already marked for elimination by the government. This would free about 1,000 controllers who could be used in more hard-pressed areas, Lewis said.

Ordering 22 of the nation's business airports to handle only 50 percent of their regularly scheduled flights over the next month. Affected cities include Atlanta, Boston, Chicago, Cleveland, Dalls-Fort Worth, Denver, Detroit, Fort Lauderdale, Houston, Kansas City, Las Vegas, Los Angeles, Miami, Minneapolis-St. Paul, metropolitan New York (LaGuardia, Kennedy and Newark airports), Pittsburgh, Philadelphia, St. Louis, San Francisco and Washington National Airport here.

Expediting the hiring and training of new controllers through beefed up programs at the FAA Academy in Oklahoma City, Okla.

Easing "bumping," no-smoking and late-arrival rules designed to accommondate passengers knocked off overbooked flights, who seek special seating or might be due compensation because of a late flight.

"This is total intimidation," said Robert E. Poli, president of the nearly 15,000-member Professional Air Traffic Controllers Organization that began the walkout Monday.

"All it's doing is making our people tougher," Poli said, adding in an interview that his members were "holding firm" in their resolve to strike until they get a new contract. The union has been without a ratified agreement since March 15.

The only point of agreement between the two sides yesterday was the number of controllers stil on strike. Poli put the figure at 12,172 late yesterday afternoon, down from 13,000 since the illegal walkout began. Lewis and Helms agreed yesterday that the number of people still on strike was "about 12,000."

In any case, Poli insisted that the government "could not make the system run safely" without controllers to whom the administration has sent about 6,000 dismissal notices. Poli accused the government of using medically disqualified controllers and working supervisors and non-strikers on excessive overtime.

Union leaders said alleged use of unqualified controllers has contributed to several "near-misses," such as one that supposedly occurred yesterday at Boston's Logan Airport. FAA officials denied that the incident, in which a transatlantic liner aborted a landing, was a "near-miss" or indicated control problems.

"At least 75 percent of the nation's 14,200 daily scheduled commercial flights were taking off and landing without problems, helms said. "Basically, the airlines and particularly the commuter carriers need only one thing, and that's passengers," Helms said.

But if the airlines were worried about the strike's fallout, so were many public and private sector unions. Despite the apparent solidarity of PATCO's ranks, there is increasing fear among labor leaders that the strike can only end badly, especially if the administration strips PATCO of representational rights. The Federal Labor Relations Authority on Monday will hold hearings that could lend to the union's decertification.

It would mark the first time in U.S. labor relations that a national public union has been permanently stripped of its representational rights, according to federal officials.

Poli, whose union is a subsidiary of an AFL-CIO affiliate, sent a telegram to federation-member unions yesterday urging them to "publicly join our fight" and to "honor our picket lines." It marked the first time since the strike began that the PATCO president publicly appealed for help from other unions.

However, Lane Kirkland, president of the AFL-CIO, said that while the AFL-CIO supports the strike, it is up to individual unions to decide if they want to honor PATCO picket lines.

"It is all very well to be a midnight gin militant to stand up and call for general strikes," Kirkland said. "But member unions will have to make their own decisions. I am not going to make the appraisal."

Kirkland added at a news conference that he believes the public is backing the Reagan administration's decision to fire striking controllers, but that support could evaporate as the strike goes on.

"I expect our people to act like trade unionists," said William Winpisinger, president of the International Association of Machinists and Aerospace Workers. "I expect them not to cross a picket line if they confront it," he said.

Charges of striker violence and harassment of nonstrikers began surfacing yesterday. Six shots reportedly were fired at an FAA facility in Oakland, Calif., and a fire allegedly was set at a radar building in Columbia, S.C., Lewis told reporters.

He also said death threats have been made against nonstrikers and their families, and the numerous instances of other harassment, beating on cars, for example, have been reported to his office.

"We have notified the Justice Department, the FBI and local authorities," Lewis said, adding that his interest was in protecting people on the job.

Poli and other union officials denied that their members were engaging in violence. Poli said, as he has before on Capitol Hill, that he would cooperate with authorities in prosecuting any union member participating in violence.

The AFL-CIO and several members of Congress were attempting to restart negotiations that broke down shortly before 2:30 a.m. Monday when the union reject the government's second settlement offer.

But Lewis, honoring his mandate from President Reagan, yesterday repeated his intention not to reopen negotiations under the pressure of an illegal strike. "Technically, they're still on strike," Lewis said, using the qualifier because of all of the strikers technically are employed for seven days after they receive their dismissal notices.

Controllers receiving the notices of termination must respond to their employing agency, the FAA, within seven days. At the end of that period, they will receive a written decision on their case. If they are fired, the decision also would contain the effective date of their termination. Poli said he will fight any terminations in court.

"If they were on vacation or sick, or something like that," that would be considered in the disposition of their cases, Lewis said.

At issue in the dispute are time and money. The union is asking for a $10,000 a year more increase. The average controller now makes $33,000 a year. The union wants a work-week reduction, from 40 hours to 32, with no reduction in pay, and an improved retirement plan.

Millions of dollars of court-imposed fines are mounting against the union, but PATCO attorney Richard J. Leighton said the union has not been counting. "Once you get beyond a certain point, it just doesn't make any difference," Leighton said.