In a statement late Monday, Johnson said the inspector general of the Transportation Security Administration (TSA), which is responsible for security at America's airports, had found "specific vulnerabilities" in screening procedures.
Though he did not elaborate, ABC News reported that an internal TSA probe had found massive security failings in some of America's busiest airports, where investigators were able to smuggle mock bombs or weapons past security a staggering 95 per cent of the time.
In one case, a screening officer failed to find a fake plastic explosive taped to an investigator's back, even after a pat-down, ABC said.
"We take these findings very seriously in our continued effort to test, measure and enhance our capabilities and techniques as threats evolve," Johnson said.
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"I have directed TSA leadership to immediately revise its standard operating procedures for screening to address the specific vulnerabilities identified by the Inspector General's testing," he added.
Johnson reassigned Melvin Carraway, the TSA's acting head, and replaced him with another interim director, Mark Hatfield.
President Barack Obama has nominated Coast Guard Vice Admiral Pete Neffenger to be the TSA'a next administrator, but he is awaiting Senate confirmation.
Additionally, Johnson ordered new training for TSA officers and the testing and evaluation of security equipment.
"Last fiscal year, TSA screened a record number of passengers at airports in the United States, and, at the same time, seized a record number of prohibited items," Johnson said.
"TSA and the Inspector General are constantly testing and adapting the systems we have in place as part of our commitment to aviation security."
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