The prisoner asked that the Israeli Justice Ministry's unit that investigates police open a case against the prisoner's investigators in the Shin Bet security service, Haaretz reported Thursday.
The petition was filed more than 16 months after the prisoner filed a complaint of torture in which he alleges he sustained physical and psychological injuries.
Haaretz said the Justice Ministry hasn't completed its preliminary investigation or responded to the prisoner's request.
The petition was filed for an unidentified inmate by the Public Committee Against Torture and by Physicians for Human Rights.
The petitioner is accused of murder and attempted murder because of his membership in a Hamas cell that has been accused of murder, Haaretz said. He has denied the charges.
In the petition, the attorneys said Shin Bet admitted using the methods of torture described in the petition and which have been prohibited by the High Court of Justice.
They said the State Prosecutor's Office confirmed that "special methods" were used on their client, including "a number of full kneeling"; "a number of lifting the hands to the back" during which the prisoner stands for long periods with his hands raised; and "a number of standings" in which the inmate stands up then sits repeatedly.
The prisoner also alleged he experienced painful handcuffing for hours, sleep deprivation, shaking, loud noises, poor nutrition, insults and threats against his family, Haaretz reported.
The state hasn't submitted its response. Representatives for Shin Bet, the Justice Ministry and the Israel Prison Service said they received the petition this week.
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