The blaze erupted around 5.45 am in the supermarket located on the ground floor of the Panaji bus stand. The area has been cordoned off and it took 10 to 12 fire tenders over three hours to control the fire, an official said.
"There has been a major damage to enforcement and registration sections and old records could have been lost in the fire. Our digitised records are, however, safe. We will have to shut down the office for a few days," Director of Transport Nikhil Desai told reporters.
A short-circuit in the supermarket is suspected to have caused the fire which spread to the transport department's office on the first floor, Mr Desai said. "An inquiry has been launched into the incident," he added.
According to news agency IANS, Goa Chief Minister Manohar Parrikar visited the Panaji bus stand, which is the state's biggest bus station and used by thousands of commuters for intra-state and inter-state travel.
(With inputs from agencies)