Airport screeners are calling out sick in increasing numbers, while some workers are fretting about where their next paycheck will come from as a partial U.S. government shutdown enters its third week.

The impact from thinner ranks at the country's airports has had a minimal impact so far, according to the Transportation Security Administration, but the agency warned that travelers may have to wait longer at security lines. Standard wait times are 30 minutes for standard checkpoints, and 10 minutes for TSA's PreCheck.

"We have seen some call outs over the holiday period and they have increased, but are causing minimal impact given there are 51,739 employees supporting the screening process," the TSA told CNBC in a statement.

"Wait times may be affected depending on the number of call outs, however to date, screening wait times remain well within TSA standards," the statement read.

TSA agents, air traffic controllers and customs and immigration officials, which screen travelers coming into the country, are among the some 420,000 federal employees who are still required to work amid the shutdown without pay. Other employees were furloughed.

Unions representing air traffic controllers and pilots from JetBlue Airways, United Airlines, Delta Air Lines and other carriers have urged the government to come to a quick end to the partial shutdown. They complain that the impasse is hindering federal safety oversight activities.

"The nation's airspace system is a complex transportation network that involves government and industry partnerships to function properly, and the disruptions being caused by the shutdown are threatening the safe operations of this network," the Air Line Pilots Association wrote in a Jan. 2 letter to President Donald Trump.

Union officials told CNN, which first reported that more TSA workers were calling out sick, that more workers could call out if they miss paychecks next week.

On Saturday morning, lines were short at John F. Kennedy International Airport. However, some federal aviation security workers said they were worried about the shutdown, and whether they would get their scheduled paycheck next Friday.

One two-year TSA agent said he canceled his cable service, and planned to look for a customer service job if he isn't paid by the end of the month.

"It's terrible," he said, speaking on the condition of anonymity because he was worried about losing his job. "You just got to deal."

The agency said that "TSA is grateful to the agents who show up to work, remain focused on the mission and respectful to the traveling public as they continue the important work necessary to secure the nation's transportation systems."

A Customs and Border Protection officer who screens passengers coming into the United States, told CNBC that "people are suffering" but that officers are still showing up because "we took an oath." He spoke on the condition of anonymity because he was not authorized to speak to the media.

Another TSA agent said he was ready to dip into his savings to make ends meet if funding doesn't materialize so his paycheck is issued by next Friday.

"Everyone should have a plan for this stuff if you work for the federal government," he said.