The Federal Aviation Administration said staffing issues were causing delays at several airports, including Newark and Denver, on Monday, just hours after the top US transportation official said air traffic controllers calling in sick had risen slightly since the government shutdown began.

Some 13,000 air traffic controllers and about 50,000 Transportation Security Administration officers must still turn up for work during the shutdown.

They are not being paid, and controllers are set to miss their first paycheck on October 14.

Transportation Secretary Sean Duffy said that at times, air traffic staffing has been cut by 50% in some areas since the shutdown started last week.

The FAA said air traffic control staffing issues are impacting flights at numerous airports, including Newark, Phoenix, Denver, Las Vegas and Burbank.

FlightAware said more than 4,000 flights in the US on Monday have been delayed, including 29% arriving flights at Denver, 19% of Newark flights and 15% of Las Vegas flights.

Weather issues are also impacting flights.

President Donald Trump has made transportation a focal point in a government shutdown battle with the Democrats, cutting off more than $28 billion of aid for climate programmes, subways, tunnels and mass transit in Democratic-leaning states, including New York and Illinois.

Delays will result from the reduced staffing, Duffy said, adding that if sick calls increase, air traffic flow will be cut to a rate that maintains air safety.

Duffy and the president of the National Air Traffic Controllers Association spoke at a press conference at Newark Liberty International Airport to discuss the effects of the shutdown.

The airport is one of three serving the heavily Democratic-leaning New York metropolitan area and is a major United Airlines hub.

Duffy noted that controllers are worried.

“They’re thinking about, am I going to get a paycheck?” Duffy said, adding that some are asking themselves: “Do I have to take a second job and drive Uber when I’m already exhausted from doing a job that’s already stressful?”

The union on Monday reminded workers, “participating in a job action could result in removal from federal service,” and that it is illegal.

“It is more important than ever that we rise to the occasion and continue delivering the consistent, high-level of public service we provide every day,” the union told members.

“We cannot stress enough that it is essential to avoid any actions that could reflect poorly on you, our union, or our professions.”

In 2019, during a 35-day shutdown, the number of absences by controllers and Transportation Security Administration officers rose as workers missed paychecks, extending checkpoint wait times at some airports.

Authorities were forced to slow air traffic in New York, which put pressure on lawmakers to quickly end the standoff.

Then-House Speaker Nancy Pelosi, a Democrat, said at the time the shutdown was “pushing our airspace to the breaking point.”

Airline trade group Airlines for America, which represents United, Delta Air Lines, American Airlines, and Southwest Airlines, warned that during a funding lapse, “the system may need to slow down, reducing efficiency,” and impacting travellers.

A persistent shortage of controllers has delayed flights, and many are working mandatory overtime and six-day workweeks.

The FAA is about 3,500 air traffic controllers short of targeted staffing levels.