Sheikh Mustafauddin, who was found with critical burn injuries at garrison area in Mehdipatnam in the heart of the city Wednesday, died at DRDO Apollo Hospital.
The body was shifted to government-run Osmania General Hospital for autopsy. Police have tightened security around the military area to prevent any untoward incident.
The boy, a student of a madarsa, told a magistrate in his dying declaration that some army men poured kerosene over him and set him ablaze.
A resident of Siddiq Nagar, Sheikh was called inside the garrison area by two military men. They allegedly beat him and later set him ablaze. He sustained 90 percent burns and was found lying near the main gate of the garrison.
A case of attempt to murder was registered against unidentified military men at Humayunagar police station. It will now be turned into a murder case.
Police formed a special team to conduct the investigation. Hyderabad police commissioner Mahender Reddy said the guilty will not be spared.
The incident led to tension in the area as people came out on streets to stage a protest against the military personnel. Police used baton charge the protestors to disperse them.
The army authorities have denied involvement of any military man in the incident.
"On investigation, it is found that this allegation is absolutely false and no army personnel is involved in this incident. The army condemns this act. All necessary assistance is being provided to the police authorities to carry out a detailed investigation to arrive at the truth," said a statement from the army authorities.