The moves follow media reports that checkpoint screeners failed to detect mock explosives and weapons in 95 percent of tests carried out by undercover agents.
Johnson said in a statement that Melvin Carraway would be reassigned to serve in the Office of State and Local Law Enforcement at Department of Homeland Security headquarters, while TSA Acting Deputy Director Mark Hatfield would lead the agency until a new acting administrator was appointed.
Airport screeners, who are employees of the TSA, did not detect banned weapons in 67 of 70 tests at dozens of airports, ABC News said, citing officials briefed on a report by Homeland Security's inspector general.
Johnson, whose department oversees the TSA, was briefed last week on the trials, which were completed recently, ABC News said.
In one test, the network said an undercover agent was stopped when he set off an alarm at a checkpoint but that TSA screeners then failed to find a fake explosive device taped to his back when they patted him down.
Johnson issued a statement on Monday saying the results of the security checks were classified but that he had directed the TSA to revise screening procedures "to address specific vulnerabilities identified" in the undercover operation. He also ordered training for all TSA officers and supervisors across the country and testing of airports' screening equipment.
Johnson said there would be more random covert testing at checkpoints.
"The numbers in these reports never look good out of context but they are a critical element in the continual evolution of our aviation security," Johnson said. "We take these findings very seriously in our continued effort to test, measure and enhance our capabilities and techniques as threats evolve."
