The shortage of air traffic controllers, who were not furloughed, was so dire during the shutdown that the Federal Aviation Administration was forced to reduce flights by 10% at 40 airports -- leading to thousands of flights being canceled and delayed across the country.
As many as 15-20 resigned during the shutdown, according to the Transportation Secretary Sean Duffy.
Duffy told reporters Tuesday that air traffic controllers will get 70% of their back pay within 24 to 48 hours of the reopening. He noted that more traffic controllers were showing up for work, as there were only four staffing triggers compared to 81 on Saturday.
MORE | Transportation Secretary Duffy says more pain to come before air traffic is back to normal
Duffy appeared at Chicago O'Hare International Airport on the same day the FAA increased its requirement of airlines to cut 6% of all domestic flights.
Amid the shutdown, Trump said in a social media post on Monday that he was recommending a $10,000 bonus to air traffic controllers who did not take any time off during the shutdown, though he did not provide specifics on how that would be done.
To those who took time off, he said, "I am NOT HAPPY WITH YOU," and called for them to leave the profession "with NO payment or severance of any kind," despite ongoing staffing shortages.
Once the Department of Transportation sees staffing levels return to pre-shutdown levels, it will ease the 10% flight cuts.
It is still unknown how the controllers will respond to the shutdown's waning hours.
When will flights go back to normal?
It is not immediately clear how long it will take for flights return to their normal schedules and capacity once the spending bill is signed.
When asked on Monday by ABC News White House correspondent Karen Travers if he could guarantee to Americans that travel will go back to normal once the government re-opens, Trump responded, "It'll go better than normal," and talked about upgrading technology in control towers, though he did not address the personnel issues.