A police commander at the Pul-e Charkhi prison, Abdul Halikm, says police fired on inmates as they tried to break through a gate. He said the authorities had urged the prisoners to move into a newly refurbished wing of the jail, but the inmates refused.
Another police officer quoted by Reuters said police opened fire after inmates tried to attack them.
It was not immediately clear if there were any casualties.
Sebghattullah Mujaddadi, a former president and the man heading talks with the prisoners, said the prisoners had backed away from an agreement.
"If the talks don't give a result, then force will ultimately be used and we sent a team to pass on that message to them," Mujaddadi said.
If was unclear if this had provoked the fresh unrest.
Earlier it had seemed that tensions were easing, with inmates handing over the bodies of four people killed and 17 wounded after the rebellion broke out on 25 February.
The rioters' demands include better prison conditions and swifter hearing of their cases.