On the direction of the Telangana High Court on Saturday, forensic experts from New Delhi's All India Institute of Medical Sciences (AIIMS) conducted the autopsy at the government-run Gandhi Hospital here.
Gandhi Hospital Superintendent Shravan Kumar told reporters that the autopsy procedure was videographed as per the court orders.
The videograph and autopsy report will be submitted to the court.
The High Court had ordered the second autopsy after Shravan Kumar personally appeared before the court and informed that the bodies will be totally decomposed in five days.
After the autopsy the bodies will be handed over to their families. The relatives, who were waiting to receive the bodies, said the last rites will be performed in their native district Narayanpur.
The court passed the orders on a Public Interest Litigation (PIL) filed by social activists K. Sujaya and others.
Mohammed Arif (26), Jollu Shiva (20), Jollu Naveen (20) and Chintakuntla Chennakeshavulu (20), all accused in the gang rape and murder of a veterinary doctor were allegedly killed by the police near Shadnagar on the outskirts of the city.
The police had claimed that the accused attacked the police party escorting them, snatched their weapons and opened fire and all four were killed in retaliatory fire by the police.
The first autopsy was conducted the same day at a government-run hospital in Mahabubnagar.
The police had taken the accused to reconstruct the crime scene at Chatanpally, where they had allegedly burnt the body of the victim on the night of November 27 after committing the gang rape at Shamshabad on the outskirts of Hyderabad.
Human rights groups had termed the encounter as extra-judicial killings and demanded a thorough probe against the policemen involved.
The Supreme Court has appointed a judicial commission to probe the encounter and submit a report within six months.
The families of the accused have also moved the apex court seeking a probe by the Central Bureau of Investigation (CBI) or any other agency and Rs 50 lakh compensation each.
( With inputs from IANS )