But he said, even the letters of reprimand handed out in nearly half of the cases are serious punishment.
Such letters can block employees from receiving a bonus or promotion, and stay with them their entire career, he told Rep. Richard Hudson, R-North Carolina, chair of the Transportation Security subcommittee.
"It's a serious thing, sir," Halinksi said. He also defended his agency's 56,000 employee workforce as overwhelmingly upright.
But Rep. John Mica, a Florida Republican and longtime critic of the TSA who requested the audit, is skeptical. He told CNN that the report shows the TSA is not doing enough to respond to and prevent misconduct.
"There's not even a way to properly report some of the offenses, so this may be just the tip of the iceberg of some of the offenses," he said.
Some other lawmakers stood by the agency Wednesday, saying the offenses represent a small percentage of TSA's 56,000 employees.
"Transportation security officers have an undeniably hard job and the overwhelming majority of them conduct themselves honorably and in accordance with TSA protocols," Rep. Cedric Richardson, D-Louisiana, said during Wednesday's hearing.
Analyst: Turn the tables on TSA
Frost and Sullivan airport security analyst John Hernandez said the report isn't particularly surprising. The TSA has been plagued by uneven training for years, he said, resulting in a work force that isn't always properly educated about how to do their jobs.
"I think John Q. Traveler should not so much be concerned, but take an active role in security," he said. "As they are willing to point out things we do wrong, we should be ready to report on the failure in their security operations, as well."
The government report calls on the TSA to improve how the agency monitors and follows up on allegations of misconduct. The agency has accepted the recommendations, Halinksi said.