TSA is working with the Atlanta airport and airlines "to maximise all available operational resources at the airport," TSA spokesman Jim Gregory said.
The agency is working with airports and airlines to consolidate operations and get the most out of resources, Gregory added.
He declined to provide absentee figures for Atlanta or other airports, saying that would compromise security by exposing possible vulnerabilities.
"Screeners will not do anything to compromise or change their security procedures," he said.
But Smith said he could relate to government workers who don't show up so they can find other ways to make ends meet.
"If I was a government worker, yes, I would probably call in and try to do something else because creditors don't care if you're furloughed or not," Smith said. "They just want to get paid and with a family of six, you have to do what you have to."
Atlanta's wait times stretched well beyond what the TSA says most passengers have encountered since the shutdown began.
Delta Air Lines, the dominant carrier in Atlanta, and other airlines said they were advising passengers to get to the airport at least two hours before domestic flights and three hours before international trips.
A Delta spokeswoman said airline employees were pitching in by helping manage TSA lines.
TSA said that it screened 1.97 million people yesterday and that 99.1 per cent waited less than 30 minutes, and 93.1 per cent less than 15 minutes. Precheck lines for people who pay a fee for expedited screening averaged less than five minutes, TSA said.
A combination of a busy travel day today combined with some security lines being closed led to the long lines, airport spokesman Andrew Gobeil said. He said he didn't know how many security lines were down.
Across the US, airports are making changes to deal with the shortage of screeners.
Miami International Airport closed one of its concourses for part of Sunday and Monday, shifting about a dozen afternoon and evening flights each day to other concourses so that TSA workers could adequately staff the other checkpoints.
Airport spokesman Greg Chin said TSA was staffing the Concourse G checkpoint today, but airport officials were monitoring the situation and would make more adjustments if necessary.
Houston's George Bush Intercontinental Airport closed the security checkpoint and ticket counters in one terminal yesterday and they remained shut today, according to an airport spokesman.
The terminal handles United Express flights. Passengers were forced to go through checkpoints in other terminals to reach their planes. A spokesman for United Airlines said flights were not affected.
- AP
