Other federal workers involved with key airport security and operations whio are going without pay include air traffic controllers and airplane safety inspectors.
Travelers could experience longer than usual lines at airports because as of Friday, around 51,000 agents won't get a paycheck.
But the impact of those absences on fliers and airport security has been hotly debated. Pre-check is funded by user fees so it is not affected by the shutdown.
The TSA is responding to staff shortages by planning to close some security checkpoints at airports nationwide beginning this weekend.
"TSA employees aren't calling out intentionally", Thomas told Business Insider last week.
TSA Administrator David Pekoske also announced Friday that workers who manned checkpoints on December 22 would be paid for their work that day and would receive a bonus for working through the busy holiday season. Both union representatives say the longer the shutdown lasts, the more employees will look for alternate work or end up calling in sick because of the burnout.
The TSA considers a normal wait time on security line 30 minutes or less.
"We're looking at a national emergency, because we have a national emergency", Trump told reporters outside the White House, in spite of overwhelming evidence that the president's dire warning is not based in fact.
As a result of the partial shutdown, the training process for new air traffic controllers has been halted, although they are desperately needed.
Democrats say Trump shut the government in a "temper tantrum" by refusing to sign bipartisan funding legislation a year ago that did not include money for his wall.
Jenniffer Gonzalez said Friday that the island still has not received $2.5 billion in funds even though more than a year has passed since Hurricane Maria hit Puerto Rico as a Category 4 storm.
However, it's a reality for thousands. Airport officials said they plan to do the same on Sunday and Monday out of concerns they wouldn't have enough employees to operate all the security checkpoints. Some have resorted to selling their possessions or posting appeals on online fundraising sites to help pay their bills.
Around that time, the union said TSA agents were starting to skip work.
Thomas is anxious about lines at major airports on the return flight if the shutdown continues.
They say the Government is also violating the Fair Labor standards.
In a before a federal court in Washington, DC the NTEU is arguing that the 1982 Antideficiency Act - under which the government shutdowns happen when Congress fails to appropriate funding for federal programs - is itself unconstitutional because it allows the executive branch to compel employees to work in emergencies.