Now, they are encouraging passengers to arrive early.
Wait times stretched as long as 70 minutes on Friday, according to officials at the airport.
Passengers said that they were told that the delays were caused by sequestration – federal cuts that have caused TSA staffing shortages.
Only 13 of 22 security lanes were used at peak travel times on Friday, officials said.
"It is unacceptable to have so few lanes open during peak passenger traffic," said Louis Miller, Aviation general manager said in a statement. "It's obvious TSA has a staffing shortage. And, it is affecting our ability to offer the level of customer service we're committed to."
Airport officials are advising passengers to arrive 90 to two hours prior to their scheduled departure times.
Extra customer services workers at the airport tried to help move lines quicker.
The TSA issued a statement saying, "While sequestration has had limited impact on Transportation Security Administration (TSA) checkpoint operations, we remain mindful of the importance of staffing to meet travel volume and providing efficient and effective screening. TSA is working to adjust its staffing models at Hartsfield-Jackson Atlanta International Airport to more closely align with anticipated passenger volume during peak and off-peak travel periods and to reduce what recently have been uncharacteristically longer wait times."