The South African Police Service (SAPS) submitted an application to the Farlam commission of inquiry on Monday for a witness dubbed Mr X to testify in-camera through a video link.
Advocate Sesi Baloyi, for the police, said the protected witness's safety would be in imminent danger if his identity was revealed or published.
"Essentially, the concern that backs up this application is that Mr X will make allegations that implicate certain persons. Those persons are presently the subject of police investigations and pending criminal proceedings," she said.
"There is a real concern that his testimony before this commission may expose him and his family to harm. As things stand, Mr X is under witness protection."
Baloyi said the inquiry led by retired judge Ian Farlam had the authority to make such special arrangement for a particular witness. She said it was "inherent" for Farlam to exclude certain members of the public from the inquiry while someone testified.
The man identified as Mr X was apparently part of a group of protesting miners that underwent a ritual at Marikana that included the burning of live sheep on the night of August 11 2012.
The rituals were a preparation for a confrontation with police, according to documents in the SAPS application. He would testify about "the killing and intimidation of Lonmin employees who were unwilling to take part in the violent strike".
Baloyi said Mr X's name would be disclosed only to the commissioners of the inquiry, and lawyers for the wounded and arrested miners, but they could not disclose it to anyone.
When Mr X testified, the police wanted only the commissioners, lawyers, and accredited media to be present in the auditorium. The police proposed that Mr X testify from a remote location.
"Members of the public willing to listen to the evidence of Mr X may do so by listening to audio transmission. The media reporting on his evidence should not identify him or in any way disclose his identity," said Baloyi.
"Any video footage recording the evidence should be blurred or blacked-out so as not to disclose his identity in any way."
The police application was opposed by Dali Mpofu, senior counsel for the wounded and arrested miners, Dumisa Ntsebeza, counsel for the families of slain miners, and Anthony Gotz for the Association of Mineworkers and Construction Union (Amcu).
The inquiry is investigating the deaths of 44 people during strike-related violence at Lonmin's platinum mining operations at Marikana, near Rustenburg in the North West. The police shot dead 34 people, mostly striking mineworkers, wounded over 70, and arrested 250 on August 16 2012 while trying to disarm and disperse them. In the preceding week, 10 people, including two policemen and two security guards, were killed.
In August 2013, Farlam expressed concern about murders linked to possible witnesses of the inquiry.
"It is a matter of concern because a number of people connected to this commission have been assassinated. It is a matter which I am sure is receiving attention from the authorities," he said.
Farlam made the remarks after National Union of Mineworkers (NUM) branch chairperson William Setelele was shot dead at Marikana. Setelele had testified at the inquiry in January and February 2013.
Another NUM official Dalivuyo Bongo was killed in October 2012. The NUM branch secretary was shot six times at his home at the Wonderkop hostel complex at Marikana on October 5 last year.
He was scheduled to testify at the commission's public hearings.
At the time of Bongo's death, the NUM said he was set to present key information to the commission. Amcu's potential key witness at the inquiry Mawethu Steve was killed in a tavern in May 2013 before he could testify. His death triggered suspected reprisal hits on two NUM members – twin brothers – the same evening.
Another Amcu leader's decomposed body was found near an Xstrata mine in neighbouring Limpopo province in June 2013 with his hands and feet tied.
The sangoma who apparently performed the rituals on the Marikana mineworkers was shot and killed in Bizana, Eastern Cape in March 2013. Alton Joja (69) was at his home when several armed men confronted him, police said at the time. – Sapa