No injury or casualty was reported in the mishap.
The blaze erupted around 5.45 am in the supermarket located on the ground floor of the Panaji bus stand.
Around 10 to 12 fire tenders rushed to the site and managed to control the blaze after hectic efforts for over three hours, the official said.
A large number of records of the state transport department were burnt in the inferno, he said.
The area was cordoned off and the losses were estimated to be worth over Rs 1 crore, said Darryk Natto, the managing director of Kadamba Transport Corporation Limited (KTCL), which owns and manages the Panaji bus stand.
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An official of the transport department said they will have to shut down their office for the next few days as important records got burnt in the flames.
"Two of our major sections dealing with enforcement and registration of vehicles were damaged in the fire. We will have to shut down the office for another three days," state transport director Nikhil Desai told reporters outside the site of the mishap.
"At least 10 to 12 fire tenders were pressed into service to control the fire. The records inside the office were burnt," he said.
"We are fortunate that the department had recently shifted a few of its services online," Desai said.