A new set of Transportation Security Administration protocols are causing the pre-summer rush of airline passengers to deal with exhaustive wait times and even miss their flights in some cases.

Passengers tell News 12 that security checkpoint lines have a wait time of over 90 minutes at LaGuardia Airport, with long waits present at other airports in the New York area.

According to the Airline Association of America, one airline last month reported that 6,800 passengers missed their flights. Twenty-two U.S. airports have now fired the TSA and installed private security agents to expedite check-ins.

The cause, officials say, is a new TSA check-in procedure that has been put in place for security purposes.

News 12 has learned the TSA cannot hire more agents because it does not have budget approval from Congress, meaning it must make do with its current numbers. The agency also attributes the longer wait times to more people traveling.

"The rise in checkpoint wait times is fueled in part by the rapid growth in travel volume, with volume up more than 7 percent over the last year," the TSA says in a statement.

The TSA adds that it is using all available means to speed up the check-in process.