The findings, leaked to the British newspaper The Guardian, said the alleged rough treatment of injured protesters also included a lack of sterilization, beatings by doctors and nurses, and being locked in basements.
A spokesman for Human Rights Watch said the findings were an indictment of the military's role in the Arab Spring protests that toppled Mubarak.
"The army always said they took the side of protesters and never fired a bullet against them," said Heba Morayef, director of the organization in Egypt. "This report is the first time that there has been any official condemnation of the military's responsibility for torture, killing, or disappearances."
The Guardian said the investigation, commissioned by President Mohamed Morsi, focused on clashes between protesters and authorities in Abbassiya in May 2011. The injured were brought to Cairo's Kobri el-Qoba military hospital where, according to a physician who was there at the time, protesters were assaulted and verbally abused by the staff under orders from military commanders.
The doctor added army brass "ordered doctors not to give any sorts of anesthetic during treatment or stitching. He also ordered that their wounds should not be cleaned."
The Guardian said the findings could place Morsi in the uncomfortable position of further investigating the powerful military hierarchy in Egypt, but human rights activists insisted the report be made public and the offenders prosecuted.
"This report is not being regarded as it should be," said Mohsen Bahnasy, a human rights lawyer, and member of the 16-member committee that compiled the report. "There is new evidence that needs to be investigated and none of that has happened."