Al-Hakim’s body expected to be taken to Qom before being flown to Iraq for burial in Najaf.
Around 4,000 people were initially arrested over protests following the June 12 poll in which Ahmadinejad was re-elected.
More than 100 pro-reform activists and politicians, including many who have made public confessions, are currently on trial for seeking a “soft overthrow” of the government.
Human rights groups and others say protesters were coerced into making public confessions through threats and abuses while they were in custody.
Ahmadinejad has denied any government involvement, saying: “These actions that were carried out in custody … were part of the enemy’s scenario.
“Security, military and intelligence forces are free from these shameful acts.”
Hundreds of thousands of people took to the streets following the election to take part in week-long protests, during which dozens of people were killed.
The president said prominent activists who are currently standing trial have to be treated with “Islamic mercy,” portraying them as having been “deceived” into taking part in the unrest.
Many pro-government figures and members of the Revolutionary Guard have publicly called for the arrest of defeated presidential candidates Mir Hossein Mousavi and
Mahdi Karroubi and former president Mohammad Khatami.
But opposition leaders including Mousavi and Karroubi have condemned the “show trials”, refusing to recognise Ahmadinejad’s presidency and vowing to continue