The Department of Homeland Security partially reversed course Sunday morning on an order that had suspended the TSA PreCheck and Global Entry airport security programs as a result of staffing shortages caused by the partial government shutdown.

“TSA PreCheck remains operational with no change for the traveling public,” the Transportation Security Administration said in a social media post. “As staffing constraints arise, TSA will evaluate on a case by case basis and adjust operations accordingly.”

A DHS official told the Washington Post that Global Entry would remain halted. The reversal was “based off of conversations the secretary had with the White House and TSA,” the official said.

TSA PreCheck and Global Entry are popular programs that give approved participants a fast-track through bag check and passport control.

The reversal came after air transport groups voiced their opposition to program closures. TSA PreCheck has around 20m enrolled users; and Global Entry is used by over 10 million pre-approved, low-risk, international travelers, including US citizens and green card holders.

Chris Sununu, president and CEO of the trade association Airlines for America, said in a statement that the group “is deeply concerned that TSA PreCheck and Global Entry programs are being suspended and that the traveling public will be, once again, used as a political football amid another government shutdown”.

“The announcement was issued with extremely short notice to travelers, giving them little time to plan accordingly, which is especially troubling at this time of record air travel,” he added.

Geoff Freeman, head of the US Travel Association, accused Democratic and Republican lawmakers of putting politics first. “Air travel is essential for our economy and daily life, and it’s disgraceful for travel to be used as leverage in political disagreements,” he said in a statement.

After the PreCheck system was restored, Freeman said in a statement that his group was “glad” DHS had avoided “a crisis of its own making”.

“We are urging the same for Global Entry,” he added. “These Trusted Traveler Programs strengthen aviation security and improve screening efficiency. They are funded by user fees, and there is no reason at this time for them to be suspended.”

The popular government programs at US airports accelerate security lines and make travel slicker for all. The suspension from early Sunday was destined to cause headaches for passengers – combined in the north-east with an incoming blizzard.

The homeland security secretary, Kristi Noem, said in a statement that “shutdowns have serious real world consequences”. She said also that “TSA and [Customs and Border Protection] CBP are prioritizing the general traveling population at our airports and ports of entry and suspending courtesy and special privilege escorts.”

TSA’s PreCheck program allows approved passengers through a faster security lane at US airports and is designed to reduce wait times. Global Entry expedites US customs and immigration clearance for pre-approved, low-risk international travelers entering the US.

A similar shutdown last year caused losses of more than $6bn across the travel industry and related sectors, he said.

The partial government shutdown began on 14 February after Democrats and the White House were unable to reach a deal on legislation to fund DHS. Democrats have been demanding changes to immigration operations that are core to Donald Trump’s aggressive mass deportation campaign.

Democrats on the House committee on homeland security have criticized the decision about airport security.

They said on social media the administration was “kneecapping the programs that make travel smoother and secure” and accused them of “ruining your travel on purpose”.

Senator Andy Kim, a New Jersey Democrat, said Noem’s actions are part of an administration strategy to distract from other issues and shift responsibility.

“This administration is trying to weaponize our government, trying to make things intentionally more difficult for the American people as a political leverage,” he told CNN on Sunday. “And the American people see that.”