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By Jay Blackman and Minyvonne Burke

Airports across the Northeast experienced major delays Friday morning as air traffic control grappled with a staff shortage amid the continuing government shutdown, the Federal Aviation Administration said.

Later Friday, President Donald Trump announced a short-term deal to reopen the government, but not before causing chaos at many of the nation's airports.

"It is wonderful news that the there is a deal to end this senseless shutdown, and the lockout of nearly a million Americans from their jobs or their paychecks," the Association of Flight Attendants-CWA said in a statement. "This never should have happened and it must never happen again. It should be abundantly clear to the American people that federal workers are not faceless bureaucrats."

The FAA said on its website Friday morning that flights at LaGuardia Airport in New York City were being delayed almost 90 minutes, and urged travelers to check the site to see if they are affected. By 4:15 p.m., delays were nearly 75 minutes, the FAA said.

The delays at LaGuardia were reported just after 10 a.m. ET and were part of a ripple effect involving other airports in the region, including the Newark Liberty International Airport in New Jersey and the Philadelphia International Airport.

The delays across the East Coast could be traced to staffing shortages at air traffic centers outside of Washington, D.C., and Jacksonville, Florida, according to an official with the Port Authority of New York and New Jersey, which runs the John F. Kennedy International, LaGuardia and Newark airports.

LaGuardia was hit hardest of those three airports because their flight schedules are tilted more toward morning, the official said.

The FAA told NBC News around 1 p.m. that the system is getting back to normal as replacement controllers arrive at centers in Washington and Jacksonville center. There are, however, still residual delays in the system, especially at LaGuardia. Newark airport is seeing some delays due to wind and weather, the FAA said.

"We have experienced a slight increase in sick leave at two air traffic control facilities affecting New York and Florida," the FAA said in a statement. "As with severe storms, we will adjust operations to a safe rate to match available controller resources. We've mitigated the impact by augmenting staffing, rerouting traffic, and increasing spacing between aircraft as needed. The results have been minimal impacts to efficiency while maintaining consistent levels of safety in the national airspace system."

One traveler, Judy Antell, has been stranded at LaGuardia since early Friday. The New York-based writer told NBC News in a phone interview that she arrived at the airport with her husband and another relative around 9:15 a.m. ET to catch a Delta flight to Cincinnati that was supposed leave at 10:30 a.m.

When she got to the airport, Antell said she was told that the flight was canceled because of a “computer glitch” and they would be put on a 2 p.m. flight.

Antell said that flight is also delayed, and Delta has not provided an update on when it will leave.

“There’s no plane here,” she said. “Everybody just seems very frustrated.”

Antell said she and her family are heading to Cincinnati to celebrate her mother’s 90th birthday.

“She might be 91 by the time we get there,” Antell told NBC, saying she and her family have been waiting in the Delta Lounge at LaGuardia until they can board their plane.

Delta Air Lines said in a statement that is experiencing roughly 200 flight delays at LaGuardia due to the FAA's Ground Delay Program.

"Delta is working to re-acommodate customers to their destinations," the company said.

The National Air Traffic Controllers Association said in a statement that they do not "condone or endorse any federal employees participating in or endorsing a coordinated activity that negatively effects the capacity of the National Airspace System or other activities that undermine the professional image and reputation of the men and women we represent."

Rep. Dan Kildee, D-Mich., warned of possible issues at airports, saying on CNBC prior to Friday’s disruptions that the only way to fix the problem is to reopen the government.

“There are real consequences to this shutdown,” he said. “Do you want your air traffic controller, for example, who's already engaged in a pretty highly stressful activity, having the additional worry of not being able to pay his or her mortgage or rent or having enough food on the table? Add that stress to that stressful job, of course at some point in time it's going to have an impact.”

“But I think more immediately what we'll see is a slowdown,” Kildee said, adding: “We just have to open the government.”

"This is exactly what AFA and other aviation unions have been warning would happen," Sara Nelson, president of the Association of Flight Attendants-CWA, said in a statement.

The massive flight delays come days after unions for air traffic controllers, flight attendants and pilots warned of safety concerns as airports across the country deal with staffing issues as a result of the partial government shutdown. The shutdown entered day 35 on Friday and is now the longest in U.S. history.

“We have a growing concern for the safety and security of our members, our airlines, and the traveling public due to the government shutdown," the presidents of the National Air Traffic Controllers Association, the Air Line Pilots Association, International, and the AFA-CWA said.

White House press secretary Sarah Sanders said that President Donald Trump was briefed on the airport delays.

"We are in regular contact with officials at the Department of Transportation and the FAA," she said.

Commerce Secretary Wilbur Ross said Thursday that he didn’t understand why air traffic controllers would call in sick because "they are eventually going to be paid."

“Well, I do worry about safety,” he told CNBC. “And it's kind of disappointing that the air traffic controllers are calling in sick in pretty large numbers.” When he was reminded that some air traffic controllers are suffering financially just by going to work, Ross said he didn’t buy that excuse because the money would eventually be there.

David K. Li contributed.