Hundreds of flights at Newark Liberty and LaGuardia airports were delayed Friday because of an increase in sick leave, causing staff shortages at two air traffic control facilities, the Federal Aviation Administration said.

The delays, aimed at spacing out flights so they could be tracked by fewer personnel, came as air traffic controllers and thousands of other federal workers entered their 35th day of working without pay because of the partial government shutdown. On Friday afternoon, President Donald Trump agreed to reopen the government temporarily.

Flights to LaGuardia were delayed by an average of nearly 90 minutes during the day, while planes out of Newark waited up to 45 minutes to take off. Some flights to Newark also were delayed up to an hour by wind, the FAA said.

Flightaware.com reported that about 500 flights were delayed into or out of LaGuardia and about 250 at Newark.

The ripple effect of the traffic management plan in place due to the staffing shortages was felt at other airports, including Philadelphia International, where planes experienced gate and taxi delays of between 16 and 30 minutes, according to the FAA.

About 70 flight delays were reported at Philadelphia International.

Early Friday night, the FAA reported delays of 15 minutes or less for all flights at Philadelphia. Arrivals at Newark were experiencing delays of about an hour, with wind continuing to be a factor.

In a statement, the FAA said, "We have experienced a slight increase in sick leave at two facilities. We’ve mitigated the impact by augmenting staffing, rerouting traffic, and increasing spacing between aircraft when needed.

“The results have been minimal impacts to efficiency while maintaining consistent levels of safety in the national airspace system,” the statement said. “The public can monitor air traffic at fly.faa.gov and they should check with airline carriers for more information.”

The Washington Post said the statement was significant because it was the first time the FAA had reported a shortage of air traffic controllers.

The White House at the time said it was monitoring the situation.

United Airlines said it was working with the FAA to minimize the impact on its customers.

“At this point, we don’t anticipate significant schedule disruptions, but it is another good illustration of the escalating impact of the government shutdown and the need for the federal government to promptly reopen,” the airline said in a statement.

American Airlines, the biggest airline at Philadelphia International, said it had not “experienced significant impacts to our operation or schedule at this point, but continue to monitor and are working closely with the FAA.”

John Murdock, a local leader with the air traffic controllers union, the National Air Traffic Controllers Association, said Philadelphia was not seeing any controller staffing shortages.

The delays stemmed from a lack of controllers in Virginia and Jacksonville, Fla., who oversee routes between flights, he said.

Murdock said that he didn’t know anything about why there were staffing shortages in the other facilities, but that there are rules around when controllers can work. If they are sick and have taken cold medicine, for example, they aren’t allowed to work. he said.

Unscheduled absences approximately doubled this week compared with the same period last year, the Transportation Security Administration said, adding that “many employees are reporting that they are not able to report to work due to financial limitations.”

Staff writers Catherine Dunn, Juliana Feliciano Reyes, and Ray Boyd contributed to this article.