The blaze was reported from the third floor of Anusandhan Bhavan at 7:06 pm when senior ministry officials were present in the building.
The office of Minister of State for Science and Technology Prithviraj Chavan is on the second floor of the building. The officials, numbering about 60, rushed out of the building as soon as the fire alarm rang.
Fire brigade rushed 14 fire tenders to the spot. Though the fire was doused within two hours, four persons were trapped on the fourth floor of the building, who were rescued after three hours.
"Out of the persons rescued, two were brought dead at hospital," a senior police official said.
"These people were on the third floor when the fire broke out. In a bid to escape, they ran to the fourth floor where they got trapped," an official said.
A hydraulic ladder was brought to the spot but it could not reach those trapped as they moved to the backside of the building, he said.
One of the persons trapped at the backside of the building was rescued after few people along with the fire department went up to the fourth floor through stairs.
"We were at the second floor of the building when the fire broke. Since repair work with gas cutter were going on so we did not paid attention to the smoke and unaware of the blaze. We ran out when we were told about the fire in the building," said an eyewitness.