The complication, for Egypt and Italy, though largely unspoken, was that Mr. Regeni did not just bear the telltale signs of torture, but that the cigarette burns and head wounds were a signature form of abuse frequently associated with the Egyptian security forces. There was no proof Mr. Regeni had even been in police custody, and it would be out of character for the authorities to abuse a Westerner. But worries about the impunity of the Egyptian security forces have been growing of late, and an initial declaration by officials that Mr. Regeni had died in a car accident also raised suspicions.

Mr. Regini vanished on Jan. 25 when, on the fifth anniversary of the uprising that ultimately ousted President Hosni Mubarak, he left his apartment for a meeting with a friend at a downtown cafe. It was a day of considerable tension in Cairo: thousands of police officers were scattered across the city to halt any antigovernment protest after a weekslong crackdown that saw the police arrest activists, shutter arts spaces and search apartments.

Friends said that Mr. Regeni was last seen walking toward his local metro station at about 7 p.m. The search to find him ramped up in recent days amid Internet appeals for information and as his parents flew to Cairo, but ended on Wednesday when his body was found on the desert highway leading to Alexandria.

Ahmed Nagy, the Egyptian prosecutor in charge of the investigation, said Mr. Regeni was naked from the waist down and with “evident signs of torture all over.” The wounds, which in addition to apparent cigarette burns included small stab marks, were “concentrated around the face and body,” Mr. Nagy said.

An autopsy completed on Thursday afternoon indicated that he had died from “internal bleeding to the brain as a result of a beating to the head.”