The blaze was noticed around 12 noon on the fourth floor of the main building, said an official of BMC Disaster Control Room.
Since Saturday is also a weekend holiday, there were no staffers in the building.
According to preliminary information, a suspected short-circuit could have caused the conflagration.
Seven fire tenders were rushed to tackle the blaze, which was brought under control a short time later.
This is the second fire in Mantralaya in the past 10 months. Last year, June 21, a major fire gutted large parts of the building killing at lease five persons, including some government staffers.
After that incident, the building has been undergoing major repairs and renovation works.