IS reportedly killed up to 600 people after seizing the jail in 2014, and was also said to have held hundreds of kidnapped women from Iraq's Yazidi minority at the facility.
The Iraqi military said that forces from the Hashed al-Shaabi - an umbrella group of pro-government forces that are dominated by Iran-backed Shiite militias - were among the units that recaptured the prison from the jihadists.
Hashed forces found "a large mass grave containing the remains of around 500 civilian prisoners in (Badush) prison who were executed by (IS) gangs after they controlled the prison during their occupation of Mosul," they said.
According to HRW, IS gunmen executed up to 600 inmates from Badush prison on June 10, 2014, forcing them to kneel along a nearby ravine and then shooting them with assault rifles.
Iraqi lawmaker Vian Dakhil also said that year that the jihadists were holding more than 500 Yazidi women at Badush.
IS targeted the Yazidi religious minority in a brutal campaign of executions, kidnapping and rape, killing men and holding women and girls as sex slaves.
Iraqi forces launched an operation to retake Mosul - the last IS-held city in Iraq - in October, recapturing its eastern side before setting their sights on its smaller but more densely populated west.
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