The incident, reported by the New York Post, occurred February 25 at the Newark Liberty International Airport as part of a training drill for the Transportation Security Administration.
The TSA would not confirm the report or the specific incident but said it regularly conducts covert testing.
"Due to the security-sensitive nature of the tests, TSA does not publicly share details about how they are conducted, what specifically is tested or the outcomes," it said.
"Regardless of the test's outcome, TSA officers are provided with immediate on-the-spot feedback so that they gain the maximum training value that the drills offer," the agency added.
The TSA is charged with screening passengers at major U.S. airports as part of sweeping security changes enacted after the September 11, 2001, attacks in the United States.
The agency was criticized this week over its decision to allow some previously banned items, such as small pocket knives and hockey sticks, back on board airplane cabins.
According to the New York Post, the undercover agent was part of a four-person team drill last month at Newark, a major airport near New York City, the main target of the 2011 attack.
The "bomber" had a mock improvised explosive device in his pants and was able to pass through a detector and even a patdown by a TSA agent, allowing him to get to the airport gate and, in theory, board a plane, the newspaper said.
In 2009, an al Qaeda-linked man tried to blow up a U.S. airliner over Detroit with a bomb hidden in a his underwear, but the plan was botched when the device failed.
Afterward, the TSA increased its use of full-body scanners to better detect explosives underneath clothing. It has since replaced the scanners with ones that allow more privacy with less life-like images.
