US President Donald Trump on Monday demanded air traffic controllers return to work as travellers endured another day of flight cancellations, which the administration ordered to manage staff shortages during the government shutdown.

Trump's comment came after the US aviation system has suffered serious disruptions in recent days as air traffic controller absences soared while they work without pay. Some are absent as they need to work second jobs or cannot afford child care.

An airline trade group said 1.2 million customers on Saturday and Sunday had flights delayed or cancelled due to air traffic issues.

Threatening to curtail the pay of any controller who did not return to work, Trump said he would award those who have not taken time off during the 41-day shutdown $10,000 bonuses and would welcome the resignations of the rest.

"All Air Traffic Controllers must get back to work, NOW!!! Anyone who doesn’t will be substantially 'docked,'" Trump wrote on social media. "REPORT TO WORK IMMEDIATELY."

Even before the shutdown, the Federal Aviation Administration was about 3,500 air traffic controllers short of targeted staffing levels. Many had been working mandatory overtime and six-day weeks.

Officials said it was unclear how the White House could deny pay under the controllers' union contract once the government reopens, as Trump threatened, or how the president would pay for the proposed $10,000 bonuses.

"I don't know - I'll get it from someplace," Trump told Fox News late on Monday.

Staffing issues at two dozen airports

There were strong indications the longest government shutdown in U.S. history will end later this week after a compromise was approved by the U.S. Senate late on Monday.

But it was unclear when Congress would give its final approval and when airline operations could return to normal as the U.S. approaches the busy Thanksgiving holiday travel period.

Some 20% to 40% of air traffic controllers have been absent on any given day at the 30 biggest U.S. airports during the shutdown, the FAA said last week.

Despite Trump's threatening social media post, the FAA reported late on Monday that it had staffing issues at nearly two dozen air traffic facilities across the United States.

The FAA imposed ground delay or ground stop programs due to staffing issues at nine airports including Houston, New York, Newark, Chicago, San Francisco, Phoenix and Las Vegas and it was slowing flights in Florida. Airlines have canceled more than 2,380 U.S. flights and delayed 8,900 on Monday, according to FlightAware, a flight tracking website.

Given how extensive the disruptions were, airline executives were pessimistic that the FAA would lift the restrictions anytime soon.

On Sunday, 2,950 flights were canceled and nearly 11,200 delayed in the single worst day for flight disruptions since the government shutdown began on October 1.

Shares of the biggest U.S. carriers, including American Airlines, Delta Air Lines and United Airlines, turned negative after Trump's social media post.

Flight cancellations set to rise

The FAA instructed airlines to cut 4% of daily flights starting last week at 40 major airports. That is scheduled to rise to 6% on Tuesday and then hit 10% on Friday.

Staffing issues worsened over the weekend and the number of air-traffic control centers with staff shortages rose to 81 on Saturday, the peak since the start of the shutdown on October 1, Transportation Secretary Sean Duffy said on Sunday.

Duffy has sought to retain controllers who could retire, speed hiring and undertake a $12.5 billion overhaul of air-traffic control systems.

Asked about Trump's comments, including the bonus plan, National Air Traffic Controllers Association President Nick Daniels said on Monday controllers would appreciate any recognition.

"We'll work with the administration .... Air traffic controllers will continue to show up during this shutdown," he said.

Trump scolded controllers who have taken time off and called those who have continued to work "GREAT PATRIOTS."

Representative Rick Larsen, the top Democrat on the House of Representatives committee overseeing the FAA, said the controllers "deserve our thanks and appreciation, not unhinged attacks on their patriotism."

'Simply unacceptable,' American Airlines executive says

Airlines urged quick approval of a bill the U.S. Senate voted to advance on Sunday that would reopen the government. It was unclear when Duffy would lift the flight restrictions.

"The government shutdown must end and so must the disruption caused to our customers and the federal employees who are being forced to work without pay," Southwest Airlines CEO Bob Jordan said.

American Airlines said more than 250,000 customers' flights were cancelled or delayed over the weekend. "This is simply unacceptable and everyone deserves better," American Chief Operating Officer David Seymour told employees.

The FAA said late on Sunday it was also suspending private-plane traffic at 12 airports with air traffic control staff shortages, including Chicago O'Hare and Reagan Washington National.