According to the Bethlehem-based prisoners' club, the detainees were protesting against their harsh living conditions at Ketziot when they clashed with guards there.
The organisation's head, Isa Qaraqa, managed to talk with detainees over the telephone and said teargas had been used to control the rioters.
Ambulances had arrived at the scene, indicating people had been injured in the clashes, Qaraqa said.
The Israeli army said it would publish an explanatory statement later on Thursday.
The Palestinian prisoners affairs ministry estimates the number of Palestinians behind Israeli bars at 5892.
Qaraqa said about 1200 Palestinians were being held at Ketziot in the Negev desert, near Israel's border with Egypt.