The Canadian government suspended 29 air traffic controllers yesterday for refusing to handle flights bound to or from U.S. airports as the American controllers' strike began causing substantial repercussions elsewhere.

The boycott by Canadian controllers, staged largely in sympathy with their American counterparts, virtually shut down air traffic between Canada and the United States and disrupted many transatlantic flights that normally fly through Canadian airspace.

For much of yesterday and last night, it seemed that the only thing flying was confusion.

The Federal Aviation Administration, dependent on information received from the Canadian Air Transport Administration, constantly juggled and rejuggled air routes in a frustrating attempt to keep transatlantic traffic moving.

Early this morning, the situation looked like this:

There was restricted air travel between the United States and Canada, and some reports indicated that U.S. flights could get into Toronto, Montreal, Calgary, Edmonton and Moncton, New Brunswick. But the reports could not be verified.

The Canadian government advised the FAA that no U.S. flights bound for Europe would be permitted in Canadian airspace after 4 a.m.(EDT) today. Such flights were to be routed south of Gander, Newfoundland, causing a slightly longer flight, the FAA said.

Flights leaving Europe for the United States also were to fly south of Gander.

"We will be able to maintain traffic east and west by using the southern routes. But there will be delays," said Linda Gosden of the Department of Transportation.

The action by many of Canada's 2,200 controllers came in conjunction with a similar move in New Zealand. Australian controllers voted to boycott U.S. flights starting at 10 a.m. (EDT) today while the Portuguese voted to do so starting at midnight (EDT) Saturday.

The Portuguese boycott would be significant because it would affect the second of two basic routes carrying U.S.-European air traffic. The other route is through Gander.

In Paris, three unions representing French controllers resumed serving U.S.-bound flights and a fourth said it was still urging members not to clear such flights, but air traffic operations were reported normal, Associated Press reported.

Britain's Civil Aviation Authority temporarily halted departures for North America. Late yesterday, some airliners grounded at London's Heathrow airport were receiving clearances to take off, but many passengers settled in the terminal for the night, AP said.

The actions mark the first concerted labor response triggered by the illegal walkout begun last Monday by 13,000 members of the Professional Air Traffic Controllers Organization.

In each of the foreign actions, controllers said they were more concerned about alleged safety problems caused by the U.S. strike than about the strike itself.

However, PATCO officials have appealed for support from foreign and domestic unions, and PATCO's leaders have been meeting with Canadian air traffic controllers periodically over the last year.

"We're in the same business," said PATCO spokesman Marcia Feldman, commenting on the meetings with Canadians.

Transportation Secretary Drew Lewis and State Department officials said yesterday they are working with the Canadian government to get flights moving again between the United States and Canada. But a State Department aide, speaking on background, said: "There's not a whole lot that we can do."

The aide said the Canadian government "is taking a firm stand" against its protesting controllers.

Unlike their counterparts in the United States, Canada's federal employes have the right to strike, but only at the end of a contract term.

Canadian transport minister Jean-Luc Pepin said at a noon press conference that the controllers could be removed from their jobs and and face fines of up to $4,000 and one year in jail for refusing to work while they have a contract.

Bill Robertson, president of the 2,200-member Canadian Air Traffic Controllers Association, said he sympathized with American controllers who have been fired, but he said he was more concerned about alleged safety problems caused by their absence.

"It is hoped this action will isolate our skies from the amateurish attempts in the U.S. to run an air traffic control system . . . ," Robertson said.

Lewis and other administration officials repeated their denials that conditions are unsafe.

Lewis said that about 75 percent of scheduled flights were taking off and landing at airports covered by the FAA's emergency "flow control" measures, and the administration's rebuilding program is proceeding. Nearly 500 military controllers are on duty and about 150 more will be pulled in by today, with 300 more expected to come aboard next week. The FAA is "negotiating with the Department of Defense" for about 2,000 military controllers to be used until civilian replacements are trained, the FAA said.

Lewis and other Reagan administration officials, including Vice President Bush and Attorney General William French Smith, yesterday again spurned PATCO President Robert E. Poli's requests to resume negotiations.

The Justice Department asked U.S. District Judge Harold H. Greene here yesterday to impose a $500,000 daily fine against the union as long as picketing and other allegedly obstructionist activities continue at air traffic control centers. A ruling is expected today.

Hearings began yesterday on a Federal Labor Relations Authority citation charging PATCO with unfair labor practices. An FLRA ruling against PATCO could lead to the union's decertification.

The FAA will meet today with airline and airport officials in what FAA spokesman Dennis Feldman described yesterday as a "sort of show-and-tell session." Feldman said the meeting is designed to find out how the system is working and what suggestions the airlines have.