Long lines are seen at a Transportation Security Administration (TSA) security checkpoint at Hartsfield-Jackson Atlanta International Airport amid the partial federal government shutdown, in Atlanta, Georgia, U.S., January 18, 2019.

The TSA officers are among the some 420,000 government employees who have been deemed essential, and have been ordered to work during the shutdown. That group also includes air traffic controllers.

The TSA said unscheduled absences on Saturday reached 10 percent of its 51,000 officers, compared with 3 percent a year ago. Many agents are calling out of work because of financial hardship, the TSA said. On the 31st day of the partial government shutdown, airport screeners have been without regular pay for four weeks.

A record number of airport security screeners, who are working unpaid amid a partial government shutdown, called out sick on Sunday, the Transportation Security Administration (TSA) said Monday.

The TSA has been calling in officers that usually help with staffing shortages during natural disasters to compensate for a rise in the absences of airport screeners.

Members of TSA's National Deployment Force have been sent to several major airports, including at Newark Liberty International airport, LaGuardia Airport, and Hartsfield-Jackson Atlanta International Airport, said agency spokesman James Gregory.

Last week, security lines in Atlanta topped an hour due to the shortage of screeners. Atlanta, the world's busiest airport is bracing for an surge in visitors when it hosts the Super Bowl on February 3.

Some federal airport personnel, working without paychecks, are facing financial strains during the standoff between the White House and Congress. On Saturday, President Donald Trump offered some legal protections for undocumented immigrants in exchange for funding for his proposed border wall in order to end the shutdown, but Democrats rejected the proposal. It suggests the impasse is unlikely to be resolved anytime soon, and could worsen the strains at airports.

The shutdown, now in its 31st day and the longest ever, has been playing out across the U.S. travel industry, where staffing shortages have led to longer airport security lines and delays in government approval for new aircraft and routes.

Gregory declined to say how many officers it was sending to other airports, but told CNBC in an email that "there are limited resources available, and our ability to reinforce airports with National Deployment Officers is becoming more difficult."

These officers are usually sent in to help cover at airports if local screeners' homes are hit by natural disasters like hurricanes and wildfires, Gregory added.

Still, most security wait times are within TSA standards. Nearly all of the 1.78 million people TSA screened on Sunday waited less than 30 minutes on Sunday, though some airports reported longer than usual wait times, the agency said Monday.

A shortage of screeners due to "excessive callouts" prompted the closure of a security checkpoint at Baltimore-Washington International Thurgood Marshall Airport on Saturday afternoon, according to the agency. The weekend's main travel headaches came from a powerful winter storm that grounded more than 2,000 flights.

Some furloughed government employees have been ordered to report back to work, even though they are still not receiving paychecks. Last week, the Federal Aviation Administration said it was calling back to work more than 3,000 aviation inspectors and engineers.

Airports, airlines and local businesses have been offering free meals to the unpaid TSA officers and other government employees working without a paycheck. Local community members have shown up at some airports with food and other donations. American Airlines' credit union is offering 1 percent loans of $1,200 or the amount of a single net paycheck to airport security workers.

—CNBC's Angelica Lavito contributed to this report.