The former police minister's lawyer says he gave no operational order.
Victims of the 2012 shooting will be remembered at a commemoration rally this weekend.
Deputy Provincial Commissioner William Mpembe appeared to have lost control of his members on the scene.
NUM says the explosive tension with Amcu is why its members will not attend the memorial.
Deal comes ahead of Marikana anniversary and alongside the launch of a forum to stop violence in the area.
Police raided hostels ahead of Friday's anniversary of the Marikana tragedy last year.