Robert Harding, a retired Army major general, took himself out of the running to become head of the airport security agency because of questions about how his former company was overpaid when the government terminated a defense contract with the firm.
It is not clear if the White House has a backup in mind for the job. But even if officials have another person on tap, internal White House reviews and background checks are likely to be even more in-depth for a third nominee.
If it takes until late spring or summer to vet another applicant, the White House will face a Congress focused on the fall election, not on approving the president's nominees.
When the administration announced Harding on March 8, it noted that the TSA position was the most important job not yet filled in the administration. Though the White House noted Saturday that President Obama remained confident in the current team at the TSA, it is once again without a permanent leader.
The Transportation Security Administration, part of the Homeland Security Department, runs the X-ray machines and metal detectors at airports around the country and sets the rules for what pieces of clothing travelers must remove while being searched. Although the TSA's highest-profile responsibilities are airports, it oversees ferries and some land transportation as well.
Erroll Southers, a top official with the Los Angeles World Airports Police Department, was nominated first by Obama for the TSA job. But Southers withdrew after acknowledging he gave inconsistent answers while his nomination was under review by the Senate.
Senate staffers reviewing the nomination had asked him questions about a reprimand he received 20 years earlier for improperly running background checks on his then-estranged wife's boyfriend.
Harding had made his career in Army intelligence and held senior positions at the Defense Intelligence Agency. The White House had hoped Harding's background in intelligence and his work after retirement running a security firm would give him the experience to run the TSA and help the government head off threats like the attempted Christmas Day bombing.
But the Senate raised questions about Harding's security company, and his nomination began to bog down.
During the early part of the Iraq war, Harding Security Associates had won a contract to provide interrogators in Iraq. The government ended the contract in early 2004. An inspector general's investigation found that the firm had claimed, and been paid, too large a termination fee. The company was forced to refund $1.8 million to the Defense Intelligence Agency.
In a statement released by the White House, Harding said that his work for his security firm had caused "distractions" that were not good for the administration.
"This was a great honor, and I felt that I could bring some leadership, vision and intelligence expertise to that position," Harding said in the statement. "Ultimately, my goal was to improve the security of our nation's transportation systems."
Nicholas S. Shapiro, a White House spokesman, praised Harding's experience but did not provide any information on when the administration would make its next nomination.
"The president is disappointed in this outcome but remains confident in the solid team of professionals at TSA," Shapiro said.