Southers had already admitted to a "grave error in judgment" 22 years ago: improperly using his position at the FBI to get a police official to run a background check on his then estranged wife's boyfriend, reports CBS News investigative correspondent Sharyl Attkisson.
In November, Southers assured Senators - under oath - it was an isolated lapse.
"Have you ever in the past misused your access to databases that the government maintains, other than the one incident that lead to this censure?" asked Sen. Susan Collins, R-Maine.
"No, Senator, I have not," Southers replied.
But a week later, Southers contradicted that account. It was in a letter he wrote to the Senate Homeland Security Committee Nov. 20, as reported by the Washington Post Friday.
Southers admitted it wasn't someone else who accessed confidential government databases, but he himself. And not once - but twice. Southers also disclosed a third apparent breach: he downloaded confidential law enforcement records in 1987 or 1988.
"We don't have a 22-year-old problem, we have a current problem with this gentleman where he can't really be up front and tell the truth," said aviation consultant Mike Boyd. "We can't have that at the top of our Transportation Security Administration."
Peter Goelz, a top transportation official under President Clinton, says the public should not be concerned.
"I think Southers, from having gone through this examination of his mistake is going to be very tough on access to private records," Goelz said.
Southers isn't talking, but the White House stood behind him Friday. With Congress on holiday break, it is too soon to know whether these revelations will hurt his chances for confirmation.