The incident has evoked widespread condemnation, with authorities announcing a probe into the matter. There were demonstrations outside the hospital with protestors seeking immediate action against the guilty.
The girl alleged that she was raped by two ward boys while she was unconscious in the operation theatre, police said after she filed the complaint with Bhoiwada police station.
The duo also verbally abused her while she was coming out of the operation theatre in a semi-conscious state, police said.
The girl, who is now five months pregnant, belongs to a minority community and is a resident of suburban Goregaon.
She was undergoing treatment at the hospital from October 4, 2006 and was operated on November 11, police said. She was discharged two months after being admitted but continued visiting the hospital regularly for check-up, police said.
After the she stopped having her periods, her mother enquired with doctors who initially told her that the period may have stopped due to 'excess blood loss and weakness'.
When she went to the hospital on April 7, Dr Mandeep examined her and informed that she was pregnant, police said. The girl, along with her parents, lodged police complaint on Saturday.
An official at the Bhoiwada police station said no arrests have been made so far.
Maharashtra Deputy Chief Minister R R Patil has asked DCP of the area to probe the matter, police sources said.