Trump Administration Starts Layoffs, Feds Start Missing Checks as Shutdown Continues

As the federal government shutdown continues the Trump Administration made good on its threat to lay off federal employees. 

About 4,200 workers were recently issued reduction in force (RIF) notices, according to a court filing. They include workers from the Departments of Commerce, Education, Health and Human Services, Housing and Urban Development, Homeland Security, and Treasury. 

Among those initially laid off were 1,200 employees at the Centers for Disease Control and Prevention (CDC). However, about half of those layoffs were reversed. Those initially fired and brought back included employees working on global health, measles and Ebola outbreaks, and suicide prevention.

“The employees who received incorrect notifications were never separated from the agency and have all been notified that they are not subject to the reduction in force,” a Trump administration official told NBC News. “This was due to a glitch in the system.”

Nevertheless, health organizations say the whiplash is demoralizing.  

“Uncertainty around which staff have been fired or rehired leaves health professionals and the public in a state of complete confusion about which longstanding public health services they can rely upon,” said a joint statement from several infectious-disease and epidemiology organizations, including the Infectious Diseases Society of America.

President Trump meanwhile said that the layoffs are targeting employees in programs “the Democrats want.”

“It’ll be Democrat-oriented because we figure, you know, they started this thing,” said the president. “So they should be Democrat-oriented. It’ll be a lot.”

Offices hit hard include HUD’s Office of Fair Housing and Equal Opportunity, the U.S. Census Bureau, and the Education Department’s Office of Special Education Programs. 

Labor organizations are challenging the legality of the layoffs in federal court in California. 

“In AFGE’s 93 years of existence under several presidential administrations – including during Trump’s first term – no president has ever decided to fire thousands of furloughed workers during a government shutdown,” said American Federation of Government Employees (AFGE) National President Everett Kelley. 

Missed Pay

Meanwhile, federal employees are receiving reduced pay checks for the first time due to this current shutdown. Civilian employees will only be paid for the work they performed in September.

The first fully missed paycheck for civilian employees will be for the October 5 through October 18 pay period if the shutdown continues. 

And President Trump directed Defense Secretary Pete Hegseth to use available funds to pay members of the military. The move takes a potential bipartisan negotiating maneuver off the table to end the shutdown. 

“I don't want folks to miss a paycheck, but I don't want just the military not to miss a paycheck,” said Senator Gary Peters (D-MI). “I want other government employees not to miss their paycheck too. We have air traffic controllers and TSA agents. I mean, just go down the list.”

Wave of Retirements

Meanwhile, a historic wave of retirements is another complication. 

According to the Office of Personnel Management (OPM), 105,000 federal employees took regular retirement during FY 2025, an 18 percent increase from the prior year. Tens of thousands of the cases are still awaiting processing, creating a challenge for HR offices across the federal government.

Making matters worse: the shutdown has furloughed some workers who handle paperwork and payroll. 

But OPM Director Scott Kupor is confident the situation is under control. 

“I’m excited about the work we’re doing, but the reality is, as you know, is there is a big volume that’s coming in a short period of time, and so we’re going to have to do everything we can to make sure that we continue to invest in those efforts that are going to significantly improve the efficiency of the process,” said Director Kupor.