The PreCheck was expected to reduce the number of agents at the checkpoint because much of the screening would be done ahead of time. This resulted in the TSA cutting its airport screener staff by 10 percent within the last three years.
But because the PreCheck program hasn't seen as many people take part as hoped, the dwindling number of agents has caused problems at the standard lines. In some cases, lines have as long as a 90-minute wait.
The chief operating officer at American Airlines said the airline has had "unacceptable" waits at many of its hubs and that the TSA said there is no relief in sight.
"Approximately 6.5 million people are enrolled in Trusted Traveler programs including TSA PreCheck and Global Entry, with more than 2 million in TSA PreCheck alone. The more people who enroll, the faster screening is for everybody," the agency said in a statement.
One of the reasons there may not be more people signing up for the PreCheck is the extra cost, which is between $85 and $100 every five years. It also takes between three to four hours to get it.
But people who have signed up for the program said, for the most part, it's worth it.
"I figure that time is money, and for me, I don't like to spend extra time in the airports if I don't have to," San Jose resident Karen Reisnvold said.
The agency is asking airlines to enforce carry-on bags restrictions before checkpoints so it has fewer bags to screen. Airport and airline staff will also take over some non-security related tasks, such as returning empty bins to the start of the checkpoint to try to resolve the wait issue until more people sign up for the PreCheck.
The TSA said the longer lines have not materialized as much in Southern California as it has in other parts of the country. But until PreCheck numbers increase, the TSA asks passengers to show up as early as two hours before their flight.
The Associated Press contributed to this report.