Thousands of air traffic controllers walked off the job at 7 a.m. yesterday, snarling air traffic across the nation and drawing an ultimatum from President Reagan, who said his administration will fire any striking controller who has not returned to work by 11 a.m. Wednesday.

"I must tell those who failed to report for duty this morning they are in violation of the law, and if they don't report for work within 48 hours, they have forfeited their jobs and will be terminated," the president said in a Rose Garden briefing shortly before 11 a.m. yesterday.

The Professional Air Traffic Controllers Organization claimed that 85 percent of its members walked out in its first nationwide strike; the government puts the figure at 70 percent. But the Federal Aviation Administration said about 60 percent of scheduled flights took to the air yesterday, with supervisors and nonstriking controllers manning radar screens.

With the addition of military controllers, officials said, the FAA could maintain the 60 percent level of flight operations indefinitely.

While passengers scrambled to rearrange flight plans or find alternate transportation, the White House immediately moved to impound PATCO's $3.5 million "contingency fund" and to decertify the union.

The Federal Labor Relations Authority (FLRA) handles labor cases affecting federal employes, and administration sources said last night that FLRA decertification cases can take as long as three weeks to decide.

In his morning briefing, Reagan made it clear that the administration intends to make good on its threat to prosecute controllers who strike in violation of federal law.

"I can't emphasize too much how strongly he feels about this," a White House aide said later. "I have never seen him quite so emphatic.He sees it really as desertion in the line of duty.

"He's tough as nails on this."

The aide said that Reagan had debated whether to give the controllers 24 or 48 hours, deciding on the longer period because he wasn't certain that the union had gotten the word out that the strike was illegal and could mean the loss of jobs.

Federal counteraction included U.S. attorneys in 11 cities filing criminal complaints in federal courts against 22 PATCO officials and local union strike leaders.

A Justice Department spokesman said last night that the complaints were filed under Section 1918 of the U.S. Criminal Code, which prohibits strikes by federal employes.

Federal lalwyers began issuing summonses to the 22 PATCO leaders last night. "These are not necessarily arrests," the Justice spokesman said. "But if these people don't show up for their scheduled hearings, they will be arrested."

The summonses were issued in Atlanta, Boston, Chicago, Cleveland, Dallas, Houston, Indianapolis, Los Angeles, Memphis, Pittsburgh and San Francisco.

U.S. District Judge Harold H. Greene last night found the air traffic controllers union and president Robert E. Poli in contempt of a federal court order prohibiting the strike and gave union officials 24 hours to get the controllers back to work or pay a $250,000 fine.

If the strike continues through 8 p.m. Wednesday, the union will be fined an additional $500,000 by Greene's order, and then $1 million daily until Sunday, for a total of $4.75 million. The government then could seek additional court action. The potential fines would exhaust the union's "contingency fund."

Greene also ordered Poli to pay a $1,000 fine per day, beginning at 8 p.m. today, for each day the strike continues until Sunday. Greene rejected the Justice Department's request that Poli be jailed until he orders his membership to end their walkout.

Asked last night if he would abide by Greene's order to instruct PATCO members immediately to return to their jobs, Poli told reporters: "If the question is, 'Will the strike continue?' the answer is 'Yes.'"

Poli said earlier that he would not bend to court action or presidential threats in pursuit of what he called the "legitimate goals" of his union -- a shorter workweek, an improved retirement plan, better working conditions and higher pay.

"We are going to stay on strike as long as it takes," Poli said.

AFL-CIO President Lane Kirkland joined the dispute, saying the government's actions smacked of "harsh and brutal overkill." Kirkland, in Chicago for the labor federation's annual midsummer executive board meeting, said the administration's "brutal, repressive measures" were counterproductive.

The meeting ends Thursday, and Kirkland said he is planning "alternative means of travel" to return to Washington.

Almost lost in the conflict, which was developing into a dramatic test of wills between the government and what is regarded as its most militant federal union, was a singular bit of irony: PATCO was one of the few unions to break ranks with organized labor and support Reagan in the 1980 presidential race.

"It's not our desire to try to make prisoners, criminals or martyrs out of these people," said Transportation Secretary Drew Lewis, but he said that the government would not back down from its obligation to enforce the law.

"People who have not returned to work," at the designated time Wednesday "will be terminated immediately by the federal government and will not be reemployed," Lewis said. i

Lewis acknowledged that the government was talking about firing possibly thousands of people whose training cost the government up to $175,000 each and who must go through two to six years of on-the-job training before reaching journeyman status.

Nevertheless, Lewis said, the administration would stick to its firing deadline "even if we're talking about 10,000 or 20,000 or 100,000 people."

"We'll start up our training school," the secretary said, referring to the FAA academy in Oklahoma City, Okla.

Lewis said the FAA currently has 9,000 applications from people seeking controllers' jobs, which pay an average annual salary of $33,000.

However, FAA Administrator Lynn Helms noted that about 20 percent of any group of applicants "wash out," and both he and Lewis later conceded that they might have problems replacing any large group of fired controllers.

Lewis said a mass firing might leave the FAA with reduced controller manpower, "for maybe a year or two years or three years."

Said Helms: "I don't want to leave you with the impression that losing 10,000 people is going to be a piece of cake. I'm sure the secretary agrees with me. Sure, there's going to be some inconvenience. There's no question about that. But this nation cannot be held hostage."

"This country will survive" the strike, "and so will the FAA," Helms said. "We'll have difficulties, but we'll be able to handle it and we'll be able to do it safely," he said.

The union disputed the administration's claim that it could safely conduct air traffic with a reduced work force. It accused the administration of "striving to recall medically disqualified controllers to staff towers and centers," a charge administration officials denied vehemently.

The controllers' contract talks halted early yesterday morning with the two sides still more than $600 million apart. Reagan has told Lewis there will be no bargaining while the controllers are on strike.

In the White House Cabinet Room, where Reagan met yesterday with his advisers on the strike, a portrait of Calvin Coolidge hangs. Reagan and others approvingly mentioned Coolidge's handling of the Boston police strike during his administration, quoting his remark at the time: "There is no right to strike against the public any time, anywhere."