Gholam Hossein Ismaili who denies any wrongdoing in the events that unfolded on April 17 has been appointed to a senior post as head of the justice department in the capital.
According to opposition websites, several inmates at the notorious Section 350 of Evin, located in northern Tehran, were beaten after scuffles broke out at a cell block, with some of them seriously hurt and taken to hospital.
Iranian officials dismiss the accounts as inaccurate, claiming it was the prisoners who resisted an inspection and started a fight with the guards.
He said the decision was taken "40 to 50 days ago, based on merit".
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Ismaili was replaced by Asghar Jahangir, considered a close figure to judiciary chief Ayatollah Sadeq Larijani who today defended the actions of the prison authorities.
"The inspections (at Evin)... Were routine and part of legal duties. No misdeed was carried out," Larijani said.
The chief judge also warned there would be no tolerance for opposition groups using similar tactics to "disseminate lies and disrupt national security", the Fars news agency reported.
Dozens of family members of the prisoners had protested near President Hassan Rouhani's compound yesterday, demanding that he respond to the reports of mistreatment.
Rouhani is a self-declared moderate who promised greater accountability from government after taking office in August.
Amnesty International has expressed concern about the Evin incident, reporting that 100 prison guards dressed in riot gear entered Section 350.