"We have decided to withdraw charges against the incarcerated miners and will release them from prison until the further investigations are undertaken," Acting NPA head Nomgcobo Jiba told reporters in Pretoria on Sunday.
Jiba explained the decision was made after "intense deliberations" and was not final.
"The NPA wants to wait for judicial inquiry, but won't necessarily do so if a prima facie case in front of it," she said.
Jiba said some miners would be released at their next court case, which was due on Monday, while the rest would be released on September 12 once their addresses were confirmed.
Murder was added to the charge sheet against the miners last week after originally being charged with public violence, illegal gathering and attempted murder.
A deadly shootout with police occured on August 16 at Lonmin's Marikana mine in the North West during a protest over wage agreements. Thirty-four people were killed and 78 were wounded.
The miners were charged under the "common purpose" doctrine, which was frequently used by the apartheid state to implicate an entire group of people in crimes by a few individuals – in spite of those being charged on the periphery often being innocent.
The director of Public Prosecutions in the North West, Johan Smit, explained on Sunday the case of the other 10 miners who were killed a week before the shootout would be handled separately, as it occured at a different time and at a different place. He added the NPA had seven suspects for those killings.
He also said one suspect was being questioned for the killing of the two security guards.
The move comes as lawyers representing the miners were preparing an urgent court application to be brought against President Jacob Zuma, demanding their immediate release in the North Gauteng High Court on Monday.
Presidential spokesperson Mac Maharaj said via a statement the president could not "accede to the demand" and that he would wait for the Farlam commission of inquiry's recommendations before undertaking any action.