Police say Ram Singh hanged himself in Delhi's Tihar jail, but defence lawyers and his family suspect he was murdered.
Home Minister Sushilkumar Shinde described his death as a "major lapse".
Mr Singh, 33, was one of five men being held in the case, which outraged India and sparked debate about the treatment of women. They all deny the charges.
A sixth suspect is being tried by a juvenile court.
