NEW YORK -- Transportation Secretary Samuel K. Skinner's plane pulled onto a taxiway at La Guardia Airport the evening of March 9, and Skinner found himself at the end of a line of planes almost as long as the eye could see.

"The first question I asked when I got back was why, on a clear day at 9 p.m., were we 19th in line?" Skinner said.

The man who oversees the country's aviation system had run up against a modern aviation mystery. Even though air traffic has remained flat at this area's three major airports for many months, air traffic control delays are climbing rapidly at La Guardia and John F. Kennedy airports, and are threatening Newark just as that airport is experiencing a boom in international traffic.

In the first five months of this year, air traffic delays were up 47 percent at Kennedy, 45 percent at La Guardia and 11 percent at Newark.

As the peak summer travel months approach -- months also characterized by traffic-delaying thunderstorms -- airlines, the Federal Aviation Administration and local officials are bracing for the possibility that things will get worse.

"The summer peak really doesn't hit till mid-July," said Robert J. Aaronson, president of the Air Transport Association, which represents major airlines. "Clearly, if this year is not good, it gives us concern for the future."

"We have not seen significant changes since last year {in air traffic control procedures}," said Clark H. Onstad, vice president of Continental Airline Holdings Inc., formerly Texas Air Corp., which owns Continental Airlines. "Given a normal pattern, you have a possibility of just as bad a problem as last summer."

In general, the reason for air traffic delays in the New York area is known. Weather plays an important factor, especially in the summer. In the late afternoon and early evening, too many planes try to land and take off despite efforts to control the flow. Growth in air traffic from other airports in the East can also affect New York airspace. Air traffic controllers are overworked, particularly at the New York Terminal Radar Control {Tracon} facility at Garden City, Long Island, which controls all traffic approaching or departing those three airports.

Even a shift in the wind can slow departures at La Guardia because of its runway configuration. That is what caused Skinner's delay. The 5 p.m. traffic crunch stretched until after 9 p.m. Skinner was delayed 45 minutes.

But there is no obvious explanation for why delays are mounting so fast.

"We've been looking at it for six months, and we haven't identified any significant new impacts," said Stan Mathews, assistant manager of the FAA's Air Traffic Operations Service.

"I think everybody has got a notion of what it could be, but I don't think anybody knows what's going on," said David Z. Plavin, director of aviation for the Port Authority of New York and New Jersey, which runs the three airports. The Port Authority has hired a consulting firm to try to unravel the mystery.

Inevitably, any discussion of New York air traffic control turns to the New York Tracon, located in a fashionable section of Long Island where comfortable homes begin selling at something more than $500,000. It is difficult to attract beginning controllers to such a high-cost area, and even experienced controllers -- with salaries of $60,000 or more plus overtime and a special 20 percent salary bonus -- cannot live well.

The Tracon, which controls every aircraft entering or leaving the New York area, is authorized to hire 204 full-performance level controllers, but now has about 110. Another 165 are in training. The Tracon, a hotbed of union activism in the 1981 strike by the Professional Air Traffic Controllers Organization, has never recovered its strength, although it was short of controllers even before the strike.

The Bush administration appears ready, within the next 10 years or so, to move Tracons out of high-cost areas such as New York, Chicago and Los Angeles, taking advantage of modern equipment that would allow controllers to do the same job in the middle of Pennsylvania farm country that they do in the middle of Long Island.

During a visit to the Long Island Tracon, Skinner was hit by a barrage of pleas to get the facility out of town, and he appears to agree.

"Over a long period of time, you should try to move," Skinner said in an interview. "Our most efficient Tracons and air route traffic control centers -- our most efficient, easiest to recruit, happiest, most satisfied -- are those that are physically located in lower cost-of-living areas.

"With modern electronics, with modern radios, with modern telephone lines, with fiber optics and microwave, it really doesn't matter where that person is physically looking at the screen, as long as the radar's out at the right place and there's a good data link to the center.

"New York and Chicago are two of the critical areas. Los Angeles is another critical area."

In the meantime, the airlines and the Port Authority are pressing the FAA to make some fixes now. A working group made up of all affected parties meets regularly with FAA officials in New York, but the pace of action is slow in such complicated airspace, especially because no one can agree what needs to be fixed.

The last time the FAA made a major change in its procedures in the area -- the revised East Coast Plan, which created new routes into New York to relieve congestion -- it unleashed a political storm over aircraft noise. People who had not heard airplanes before, particularly in New Jersey, screamed. That controversy continues.

The FAA generally blames delays on weather problems and the desire of airlines to cram as many flights as possible into certain peak travel times.

"Typically, the biggest reason for delays in the New York area is weather," said Jack Kies, assistant manager-operations for the New York Tracon. "{And} sometimes the airports taxi out more planes than the system will handle. . . . There's something inherently wrong with a system that would blame air traffic control for something that's not technically possible."

While acknowledging that weather can be a problem, the airlines and the Port Authority say the FAA could do a better job.

"A significant part of the problem is the actual operation of the air traffic control system," said Aaronson of the ATA. "Air traffic control is an art, not a science. You can always improve your artistic performance."

Jack Ryan, the ATA's vice president for air traffic management, who is negotiating with the FAA, said he thinks managers at the New York Tracon are making a good-faith effort to do what they can.

For example, Ryan said, steps have been taken to alleviate the congestion that happens because the controller who handles arrivals and departures at La Guardia must also deal with flights from Newark passing over La Guardia. When things get busy, the controller does the safe thing and allows La Guardia flights to sit on the ground for a period. Since June 4, a coordinator is on duty during the day to help such overloaded controllers.

"They really want to solve the problem, and I'm encouraged about it," Ryan said.

Aaronson, in a March 7 letter to FAA Administrator James B. Busey, called for sending a special team to New York, setting goals and doing whatever necessary to carry them out.

"First and foremost, the staffing situation at the New York Tracon and the three towers should be addressed," Aaronson said, including establishing a contract training program for controllers, an increase in the number of beginning controllers, sufficient overtime pay and a moratorium on transfers.

Busey replied on April 6, but avoided addressing his specific suggestions.

"What you need up there is a tiger team and a headquarters guy in charge of seeing that things get done," said Onstad of Continental, which is particularly nervous because of its heavy investment in Newark as a hub. Partly because of Continental's efforts to attract foreign airline traffic through Newark, international traffic has grown 374 percent in the last decade.

"Our agenda is to see that the infrastructure is there to handle it {the growth}," Onstad said, adding that Continental is also having trouble persuading the government to adequately staff immigration and customs offices at the airport.

The Port Authority's Plavin expressed frustration with a slow pace of ordering new radar equipment that would allow more traffic to be handled in bad weather. One such system, being tested at the Raleigh-Durham airport in North Carolina, would allow simultaneous landings on closely spaced parallel runways, which now can be done only when skies are clear.

"I've committed the Port Authority to paying for them at Port Authority facilities, if {the FAA will} just do it," Plavin said. But he said the FAA has told him it will be at least six years before the new radar is ready.

Plavin said he is not concerned that delays will drive passengers away from New York airports because most traffic at the three airports is going to or from New York, not transferring.

"The concern is that it represents a lousy level of service to our customers," Plavin said. "In the long term, it's a question of whether people will see New York as a place to do business."

A delay to the Federal Aviation Administration is not the same thing as a delay to a passenger.

For most reporting, the FAA considers a flight delayed if it is late 15 minutes or more because of the air traffic control system. Delays caused by the airlines themselves are not counted, such as holding a plane for connecting flights.

A somewhat more accurate barometer of passenger delay is the Transportation Department's Air Travel Consumer Report, which reports all flights 15 or more minutes late. It has the drawback of not indicating the reason for delays. Also, by agreement, airlines are not required to report mechanical delays on the theory that airlines should not be pressured to take off in unsafe conditions.