The fire in three rooms including a strong room of the office containing cash and taxes records broke out at 1:30 am, the sources said.
The police sought the assistance of the Forensic department to investigate how the fire broke out in the highly secure building and not ruled out foul play.
According to the police, the guard of the office, B Shah, was not present when the fire broke out and reached when firefighters almost completed dousing the flames.
"We cannot rule out foul play. Samples are being taken and the matter is under investigation," a senior police officer told PTI.
Police questioned several people including the district transport officer C Lyngdoh who said that he came to know of the fire only at 9:30 when he reached the office.
Earlier, several thousand documents of the officer of the district transport office were destroyed in the same manner, the sources added.
The third secretariat also houses offices of the Electricity Commission and the Right to Information Commissioner besides others.
Shillong: A fire destroyed important records of the Meghalaya transport department at the third secretariat building here early on Monday, official sources said.
First Published: Monday, February 25, 2013, 15:02