An FAA spokesman said agents were not performing required inspections on some bags.
A spokeswoman for American Airlines said agents were testing a new bag screening procedure that matches checked bags with the passenger list and that the FAA requested the bags be re-inspected.
"And they asked that certain bags be rescreened before takeoff," Julia Bishop-Cross of American Airlines told Friday's St. Louis Post-Dispatch. "American Airlines is in full compliance with all Federal Aviation Administration orders concerning safety and security of passengers and baggage."
American flights were prevented from departing from about 7 p.m. until 9:30 p.m. Thursday forcing hundreds of passengers to wait aboard planes on the tarmac and at the concourse gates while the baggage was rechecked.
Two bomb-sniffing dogs checked luggage randomly taken off at least 35 planes at American gates but nothing out of the ordinary was found.
"We were simply providing additional manpower and dog teams to facilitate this search," said St. Louis Airport Police Chief Paul Mason. "We didn't anticipate we would find anything. There is just a regulation that requires certain things be done."
Flights that had departed earlier were not asked to return to the airport.
Beginning Jan. 18, new FAA safety and security regulations will require airlines to screen all checked baggage for explosives.
American Airlines recently implemented "positive bag matching" of checked bags as part of security upgrades ordered after the Sept. 11 hijackings.