Transportation Secretary Sean Duffy announced Wednesday afternoon that he will be reducing flight capacity by 10% at 40 major airports starting Friday morning, affecting roughly 3,500 to 4,000 flights daily.
It was not immediately clear which airports would be affected.
"This is proactive," Duffy said in a news conference.
Federal Aviation Administration Administrator Bryan Bedford said additional measures could be taken after the initial reduction.
"As we slice the data more granularly, we are seeing pressures build in a way that we don't feel, if we allow it to go unchecked, will allow us to continue to tell the public that we operate the safest airline system in the world," Bedford said Wednesday.
Bedford added that the administration will be meeting with the airline community to decide how to move forward on implementing the reduction, which he said has never happened before during his time in the industry.
The government shutdown, which entered its 36th full day on Wednesday, is now the longest in U.S. history.
Duffy said he expects more cancellations as a result of the reduction, which has no set end time. "We thought 10% was the right number based on the pressure we were seeing," he said.
The move comes as air traffic controllers have missed their paychecks due to the government shutdown. Air traffic controllers and Transportation Security Administration screeners are among the essential government employees who are required to work during the shutdown.
The closure has also raised concerns about already thin staffing among air traffic controllers, the FAA said. Insufficient staffing at some FAA facilities has disrupted some flights since Oct. 1.
Earlier this week, Duffy told CNBC's "Squawk Box" that he could "shut the whole airspace down" if the shutdown drags on.
On Wednesday morning, National Air Traffic Controllers Association President Nick Daniels told "Squawk Box" that it could take "weeks to recover" from the impacts of the government shutdown on air traffic controllers.