Rogoff is now the acting under secretary for policy. The position became available when New York City Mayor Bill de Blasio tapped previous under secretary Polly Trottenbreg as the city's transportation commissioner.
Rogoff has led FTA since May 2009. Before that, he was a longtime congressional staffer, serving 22 yeas with the Senate Appropriations Committee.
Rogoff would need to be confirmed by the Senate for the post to become permanent -- a process that could be lengthy.
The move is the latest in a series of shakeups for the department.
Last month, Deputy Transportation Secretary John Porcari, the department's number two official, resigned from office. Victor Mendez, who leads the Federal Highway Administration, was subsequently named acting deputy secretary.
Meanwhile, Friday is the final day on the job for David Strickland, the head of the National Highway Traffic Safety Administration.
