Flights at numerous major U.S. airports were delayed Friday due to an "increase in sick leave" among air-traffic controllers, the Federal Aviation Administration said.

The FAA briefly issued a ground stop at New York City's LaGuardia Airport on Friday morning, temporarily halting flights because of the staffing issues, while delays were also recorded at Newark and Philadelphia airports.

FAA spokesperson Gregory Martin said issues occurred at two air-traffic facilities: one in Washington, D.C., that controls high-altitude air traffic over seven states, and another in Jacksonville, Fla.

On Twitter, the agency said: "We are mitigating the impact by augmenting staffing, rerouting traffic, and increasing spacing between the aircraft as needed."

The issues come amid the longest government shutdown in U.S. history, which affects hundreds of thousands of federal workers, including air-traffic controllers.

Friday marks the day federal workers miss their second paycheque since the shutdown began.

White House spokesperson Sarah Sanders said in a statement that U.S. President Donald Trump had been briefed on the airport delays.

In a letter sent to Trump shortly before the delays were announced, New York Gov. Andrew Cuomo warned the president that the continuing shutdown is impacting safety and security at airports and putting travellers at risk.

Air Canada and WestJet both operate flights to LaGuardia, the airport that appeared the most affected by the staffing shortage. In Toronto, numerous delays were reported for flights headed to LaGuardia from Pearson International Airport.

Martin said safety at U.S. airports was being maintained during a period of "minimal impacts" on travel.

On Thursday, three major U.S. airlines — American Airlines, Southwest Airlines and JetBlue Airways — said the impact of the shutdown on their business had so far been limited but was nearing a tipping point.

"No one can predict what impact it will have as it continues," Southwest chief executive Gary Kelly said of the shutdown on Thursday.