In Baghdad's Rusafa facility, about 150 prisoners were being held in a room about the size of a school classroom.
Many are still being held although they have never been charged, because the judicial system is too overloaded to cope, the BBC's Andrew North says.
The interior ministry admits there is a problem, but blames the security situation for the thousands of arrests.
'Terrible conditions'
Our correspondent was taken to Rusafa prison, located in the east of the Iraqi capital, by interior ministry officials after he had asked to check allegations of torture and abuse.