The incident took place when a fire broke out in the warehouse at Chawk area of the district, about 250 kms from the State capital, the police said.
A big mishap was prevented by the immediate action of the fire fighting officials and controlling the fire from spreading in the nearby areas, police inspector Shailendra Singh said.
A short circuit was suspected to be the cause of the incident while the exact reason is yet to be ascertained.
Three employees of the warehouse who injured in the incident were being treated in the Varanasi District hospital.
The owner of the ware house is yet to be traced.