The Media Cell Security Investigation team said in a statement that one grave near the Badoush Prison site contained the bodies of 470 prisoners killed by IS. It said a second grave contained 30 victims.
A security official who spoke on condition of anonymity said based on records of prisoners who were at Badoush most are believed to have been Shiite Muslims or other minorities. The Islamic State group is a Sunni extremist group.
Authorities were continuing to look for more graves. A massacre at Badoush in June 2014 left 600 male inmates dead.
A patch of scraped earth and tire tracks show the likely killing site, according to exclusive photos obtained by the imagery intelligence firm AllSource Analysis.
The Islamic State group has scattered mass graves across Iraq and Syria.
The Associated Press last year documented and mapped 72 of them. For at least 16 of the Iraqi graves, officials do not even guess the number of dead.
In others, the estimates are based on memories of traumatized survivors, Islamic State propaganda and what can be gleaned from a cursory look at the earth. But even the known numbers of victims ranges from 5,200 to more than 15,000.
Also today, the spiritual leader of Iraq's Shiite majority called on doctors from across Iraq to help civilians fleeing clashes in the latest fight against the Islamic State group in Iraq.
The call during the Friday sermon delivered by Sistani's representative Sheikh Karbalai/174721" target=_blank>Abdulmehdi al-Karbalai, from the holy city of Karbala comes after the operation to retake Tal Afar began last week. Tal Afar sits west of Mosul, where victory was declared against IS in July.
Thousands of civilians are estimated to have been killed in the nine-month fight.