The halt in the department-run programs will begin early on Sunday after the partial shutdown began last week following Republicans and Democrats' failure to clinch a deal on immigration enforcement reforms.
"Airlines for America is deeply concerned that ... the travelling public will be, once again, used as a political football amid another government shutdown," the trade association and lobby group's chief executive Chris Sununu said.
News of the suspensions came at "extremely short notice to travellers, giving them little time to plan accordingly", he said in a statement, urging Congress to "get a deal done".
A similar shutdown in 2025 caused losses of $US6.1 billion ($A8.6 billion) across the travel industry and related sectors, he said.
"TSA and Customs and Border Protection are prioritising the general travis (Transportation Routing and Vehicle Information System) population at our airports and ports of entry and suspending courtesy and special privilege escorts," Homeland Security Secretary Kristi Noem said.
"We are making tough but necessary workforce and resource decisions to mitigate the damage," she said in a statement to Reuters.
The pause in programs is among the emergency measures the department is taking to redirect staffing more than a week after Congress failed to send it more money, the Washington Post said.
PreCheck had more than 20 million active members, the TSA said in 2024, while total vetted airline passengers in the department's traveller programs, including Global Entry, exceeded 40 million.
The PreCheck program allows approved passengers to go through a dedicated, faster security lane at US airports and is designed to reduce wait times and streamline screening.
Global Entry expedites US customs and immigration clearance for pre-approved, low-risk international travellers entering the US.
Sunday's moves follow orders from the Trump administration to another constituent of the department, the Federal Emergency Management Agency, to suspend deployment of aid workers to disaster-affected areas due to the shutdown.
