Interior Ministry spokesman Nusrat Rahimi said that the clashes raised after some prisoners refused to allow police to investigate their cells.
Several prisoners attacked on police and injured 20 members of the Afghan security forces, he said.
Following the riot, police have opened fire in the air to disperse to control the situation but some prisoners have tried to disarm security forces, he further said.
According to police, the situation of the jail is under security forces control now.
Pul-e Charkhi prison is the largest prison in Afghanistan where powerful criminals have access to drugs and mobile phones.