Department of Transportation is a building located on Gromflom Prime, which presumably is used to coordinate and plan federal transportation projects within the planet.
In the episode "Valkyrick", Rick Sanchez and Space Beth disguise themselves as bugs working for the department and meet Cisco as a apart of the former's plan in order to find and portal out a spore bomb out of the robot Gromflomite Queen. However, Cisco fails to show up and the two are forced to fight Gromflomites on the planet.