The fire broke out at around 1.30 am and destroyed at least three rooms including a strong room of the district Transport office here containing cash and tax records, the sources said.
Several important records of the Megahalaya transport department were also feared destroyed in the fire, they said.
Police have sought help from the Forensic department to investigate into how the fire broke out in the highly secured concrete building even as they have not ruled out foul play at the moment.
The third secretariat also houses other important government offices like the Electricity Commission, the Information Commission.
Shah reached the office only when the firefighters had almost doused the flames.
"We cannot rule out foul play in this incident. Samples were being taken and the matter is under investigation," a senior police officer told PTI.
Police have questioned several people in this regard including the East Khasi Hill district transport officer C Lyngdoh, sources said.
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