"Serving as FAA Administrator has been an absolute honor and the highlight of my professional career," Babbitt said in a statement. "But I am unwilling to let anything cast a shadow on the outstanding work done 24 hours a day, 7 days a week by my colleagues at the FAA."
According to police, Babbitt was arrested on Saturday after an officer in Fairfax, Va., observed his car driving on the wrong side of the road.
Babbitt was taken into custody and later released on a personal recognizance bond. He was the only person in the vehicle at the time, and he was cooperative at the time of his arrest, police said.
On Monday, the Department of Transportation, which includes the FAA, said Babbitt decided to take a leave of absence.
Deputy Administrator Michael Huerta is serving as acting administrator.