The country is suffering a protracted surge in violence that has claimed more than 2,550 lives this year, and the area west of Baghdad where the prison is located is particularly insecure.
The ministry announced online the "complete closure of Baghdad Central Prison, previously (known as) 'Abu Ghraib,' and the removal of the inmates in cooperation with the ministries of defence and interior."
The statement quoted Justice Minister Hassan al-Shammari as saying 2,400 inmates arrested or sentenced for terrorism-related offences have been transferred to other facilities in central and northern Iraq.
It was not immediately clear whether the closure was temporary or permanent.
The prison is located between Baghdad and the city of Fallujah, which has been held by anti-government fighters since early January.
Shelling in Fallujah on Tuesday killed five people and wounded 16, while mortar rounds and twin suicide bombings in Anbar provincial capital Ramadi, farther west, left one dead and eight wounded.
Abu Ghraib prison served as a notorious torture centre under now-executed dictator Saddam Hussein, with an estimated 4,000 detainees perishing there.
And in July 2013, militants assaulted Abu Ghraib and another prison in Taji, north of Baghdad.
Officials said hundreds of inmates escaped and more than 50 prisoners and members of the security forces were killed in the assaults, which were claimed by the Islamic State of Iraq and the Levant, a powerful jihadist group.
Iraq has been hit by a year-long surge in violence, driven principally by widespread anger among the Sunni Arab minority, who say they are mistreated by the Shiite-led government and security forces, and also fuelled by the civil war in neighbouring Syria.
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