Ayatollah Sadeq Larijani, Iran's new judiciary chief, appointed Abbas Jafari Dowlatabadi as the new Tehran prosecutor.
He also appointed a three-member team to supervise an investigation into the alleged abuse of detained protesters following Iran's post election unrest, IRNA reported.
More than 100 prominent opposition supporters have been on trial since August 1 on accusations of plotting to overthrow the clerical leadership through the protests that followed the disputed re-election of Mahmoud Ahmadinejad, the president, in June.
The protesters claimed Ahmadinejad won the vote through fraud and that Mir Hossein Mousavi, his nearest rival and a moderate opposition leader, was the true winner.
Hundreds of protesters and opposition activists were arrested when security forces crushed the mass protests in the wake of the vote.
The opposition says at least 69 people were killed in the crackdown, including some who died from torture in prison.
The allegations of prisoner abuse in the post-election crackdown have rattled not only Ahmadinejad's government but Iran's entire ruling system.
Claims by Mahdi Karroubi, a prominent opposition figure, that some detainees have been raped prompted criticism even from pro-government conservatives.
Mortazavi has found himself linked to alleged prisoner abuse cases in the past.
As Tehran prosecutor he was behind the announcement of false information about the death of an Iranian-Canadian journalist while in police custody in 2003.
The judiciary announced that Zahra Kazemi died of a stroke, but an investigation ordered by Mohammad Khatami, the former president, later found that Kazemi died of a fractured skull and brain hemorrhage from a blow to the head.