The incident took place at around midnight and fire fighters were busy dousing the flames till the early hours today, the police said.
The exact reason of the fire was not known immediately, East Khasi Hills Superintendent of Police M Kharkrang said, not ruling out the involvement of pro-ILP activists.
The police said people residing in the neighbourhood heard an explosion and rushed out of their homes to find that the warehouse had gone up in flames.
Telecom equipment and mobile tower materials kept at the warehouse were damaged and BSNL officials tabulated the loss to be over Rs 40 crore. Investigation into the incident was on, the police said.
Meanwhile, pro-ILP activists in Meghalaya have announced road blockade for three nights beginning from 7 PM today.
The blockade would be in force from 7 PM to 5 AM for the three days. The blockade was announced by the activists demanding immediate implementation of the ILP and against the state government's tough stand against the activists.
The state government had, instead of negotiating with the agitating NGOs, announced the setting up of a special court to deal with cases breaching the Supreme Court ruling against bandh and those disrupting public order.