A Board of Inquiry is looking into the incident that occurred early this month, the sources said, adding no loss of life has been reported.
The practice round hit the 3rd floor of the high security building when the gun went off accidentally while undergoing repair on board the warship ICGS Samrat in presence of the Mumbai-based Naval Armament Depot personnel, they said.
ICGS Samrat carries two indigenous 30mm CRN 91 Gun along with fire control system.
This is the fifth reported incident where naval assets have suffered damage including the INS Sindhurakshak accident where the vessel sank inside the Mumbai harbour after an explosion in its torpedo section.
The BoI is headed by a Commodore-rank officer from the Coast Guard and also includes two naval officers, the sources said.
In a recent incident earlier this month, the INS Talwar collided with an unlit fishing trawler near Ratnagiri coast in Maharashtra in which four fishermen suffered injuries prompting the Navy to order an inquiry.
There was also a fire incident on board the only aircraft carrier INS Viraat off the coast of Mumbai earlier this year.
INS Konkan, a newly commissioned minesweeper vessel of the Navy, also suffered damage due to a fire incident in the first week of the month in Vishakhapatnam.