Food and Drug Administration Commissioner Scott Gottlieb warned on Friday that if the partial government shutdown persists, it will force the FDA to make "hard decisions" on preserving key functions of the agency.

The FDA cannot accept any new funding during the shutdown, which entered its 28th day on Friday. That has forced the agency to stretch its remaining funding to last roughly five more weeks. In prepared remarks for delivery at a hearing Friday, Gottlieb said the shutdown has represented one of the "most significant operational challenges" in the FDA's recent history.

"We've had to make hard decisions in the last month to preserve key functions to maintain our critical consumer protection role," Gottlieb said. "As our user fee programs begin to run out of money, we have many hard decisions ahead of us."

The timeline for when the agency runs out of funds, which came in part from application fees paid by drug and device makers, could change, the FDA said earlier this week. But the agency added that the change wouldn't be more than "plus or minus a week."

Gottlieb said Friday the FDA will maintain its critical safety functions and preserve as much of its review functions as possible. "We are in uncharted territory. This is a watershed moment in the life of this agency," he added.

The shutdown has left some pharmaceutical companies in the dark regarding the submission of their drug applications with the FDA for potentially life-saving and profitable treatments.

Applications typically take months to review. Any possible delays from the agency could have huge consequences for the balance sheet of drugmakers, especially those who may be scrambling to push new, innovative drugs to the market to stay in business. Delays could also create a backlog for the agency because some drugmakers may be waiting to file applications after the shutdown ends.

The shutdown has already created consequences for one drugmaker, Aimmune Therapeutics, a California-based biotech company that develops treatments for food allergies.

Aimmune submitted an application and transferred the money needed to pay for the review for its experimental immuno-therapy for peanut allergies the day before the shutdown began. But the company disclosed in a regulatory filing this week that the FDA would not start a review for its treatment until the "shutdown and lapse in appropriations" ended.