A temporary hiring freeze for the federal workforce includes hundreds of positions at the Food and Drug Administration that aren't funded by taxpayers.

As one of his first acts, President Trump put a 90-day temporary freeze on hiring at federal agencies, with some exceptions for military and national security.

The White House confirmed to the Washington Examiner that the freeze applies to any new hires paid for by drug and device makers, through "user fees." The FDA has user fee programs for generic and brand name drugs and for medical devices and tissue-based biologic drugs.

Companies agree to pay a user fee whenever they submit new product applications, and the FDA promises in turn to use those funds to hire new staff and improve the approval process.

User fees have become a big part of the FDA, which has about 16,000 employees. They account for 68 percent of the agency's review budget for brand name drugs and 58 percent of the review budget for generic drugs, according to a report from the research firm Avalere Health.

The FDA refused to say how many user fee positions could be affected by the hiring freeze and directed inquiries to the White House.

A White House aide told the Washington Examiner that just because user fees fund a position doesn't necessarily exempt the position from the hiring freeze.

The freeze applies to all executive departments and agencies "regardless of the sources of their operational and programmatic funding," the aide said.

However, the user fee-supported work could be "subject to public safety and national security exemptions provided for by the memorandum."

The order exempts the military, but not civilians who work for the military, from the hiring freeze.

One advocate said all of FDA's positions should be classified as public safety because of their impact on public health.

"Americans need their food supply to be safe and their medical products to be safe and effective," said Steven Grossman, executive director of the advocacy group Alliance for a Stronger FDA. "Since more than 80 percent of FDA's costs are personnel-driven, FDA cannot fulfill its statutory responsibilities without a complete workforce."

Grossman wrote in a blog post that a definition hasn't been created for what is considered "public safety." He expects the federal government to issue clarifying guidance on what is and isn't affected by the freeze.

The generic drug industry is worried about the impact the freeze could have on the review of new generic drugs, pointing to a backlog of thousands of generic drug applications the FDA promised to tackle under the user fee agreement with the generic drug industry.

"A fully resourced FDA is critical to reducing the backlog," according to a statement from the Generic Pharmaceutical Association, the top lobbying group for generic drugs.

Agency insiders are also questioning how the freeze will affect product reviews.

"We have all seen the Office of Generic Drugs struggle with efforts to keep pace with the large influx of generic applications, as well as meet demanding [Generic Drug User Fee Act] deadlines," wrote Bob Pollack in a blog post for FDA regulatory consulting firm Lachman Consultants. Pollack is a senior adviser to the firm and former acting deputy director of the Office of Generic Drugs.

The user-fee programs expire at the end of the fiscal year at the end of September. Before then, Congress must reauthorize a new program with new payment rates.