At airports in Houston, New York and Atlanta, more than one-third of Transportation Security Administration (TSA) staff were calling in sick or otherwise absent, the Department of Homeland Security (DHS) said on Sunday.
The shutdown left tens of thousands working without pay while congressional Democrats and Republicans argue over the DHS budget.
To help fill the staffing gaps, hundreds of Immigration and Customs Enforcement agents will deploy to airports starting on Monday, government officials said.
DHS said on Sunday it would not publicly share details about the ICE deployment, in order to preserve operational security, but sources briefed on the matter said the current plan calls for deploying ICE agents to 14 locations, although that figure may change.
For now, ICE personnel won't be deployed in areas behind airport security checkpoints because they lack the specific clearance needed, the sources said.
Atlanta Mayor Andre Dickens said in a statement his office has been informed that ICE agents on Monday would be sent to Hartsfield-Jackson, the busiest US airport in passenger numbers.
Federal officials indicated that the ICE deployment would support TSA in crowd control and managing security lines in domestic terminals, and is "not intended to conduct immigration enforcement activities", Dickens said.
That contradicts a social media post by Trump on Saturday that ICE agents' activities would include "the immediate arrest of all Illegal Immigrants who have come into our Country," particularly Somalis, a group that his administration has accused, without evidence, of widespread fraud and corruption.
Democrats have held up funding for DHS while demanding a change in rules governing its immigration operations, which have killed US citizens and sparked public outrage.
Overall, more than nine per cent of TSA employees have been absent from work over the past seven days, leading to lengthy lines for passengers trying to get to their gates, according to DHS.
"Many TSA officers cannot pay their rent, buy food, or afford to put gas in their cars - forcing them to call out sick from work," a DHS spokesperson said on Sunday.
Hundreds of TSA agents forced to work without pay have also simply resigned, according to their union and TSA.
Border czar Tom Homan said sending immigration agents to bolster short-staffed TSA teams would speed up airport lines, but the union for TSA workers said that didn't solve the underlying problem of pay.
"When we deploy tomorrow, we'll have a well thought-out plan to execute," Homan said on CNN's "State of the Union" program.
"ICE will do the job far better than ever done before!" Trump wrote in a social media post.
