The US Justice Department said on Tuesday it would appeal against a federal district court ruling, which ended mandatory masks for travel, if the nation's health agency believed they were still necessary.
The judge ruled that the 14-month-old directive was unlawful, ending a key measure to reduce the spread of Covid-19.
The ruling meant an end to obligatory masks on airlines and transport systems across the country.
“The Department of Justice and the Centres for Disease Control and Prevention disagree with the district court’s decision and will appeal, subject to CDC’s conclusion that the order remains necessary for public health," said the agency's spokesman, Anthony Coley.
"The department continues to believe that the order requiring masking in the transportation corridor is a valid exercise of the authority Congress has given CDC to protect the public health.
"That is an important authority the department will continue to work to preserve."
Earlier on Tuesday, US President Joe Biden said that "it's up to them" when asked if people should keep wearing masks on airplanes. That was at odds with his administration's official guidance.
The CDC still advises people to wear masks on public transport, as White House spokeswoman Jen Psaki said before Mr Biden's comment.
"We're continuing to encourage people to wear masks," Ms Psaki said.
Monday's court decision means the CDC's public transport mask order is no longer in effect, a US official said.
Coronavirus infections are rising in the US, and more than 400 people are dying daily from the airborne disease, based on the latest seven-day average.
There have been a series of judgments against Biden administration directives to fight Covid-19 — which has killed nearly 1 million people in the US — including vaccination or Covid testing mandates for employers.
"Public health decisions shouldn't be made by the courts. They should be made by public health experts," Ms Psaki said.
The new White House Covid-19 Response Co-ordinator, Dr Ashish Jha, tweeted on Tuesday that the judge's ruling "was deeply disappointing".
Dr Jha agreed that health decisions should lie with the agency.
"CDC scientists had asked for 15 days to make a more data-driven, durable decision," he said. "We should have given it to them."
News agencies contributed to this report
