"The decision is based on the fact that there was consensus between the NUM, Association of Mineworkers and Construction Union [Amcu], Solidarity, Uasa [United Association of SA], and various other stakeholders, including the mining companies, that deputy president of the country Kgalema Motlanthe's office would organise the commemorations," spokesperson Lesiba Seshoka said in a statement.
"The organisation of these commemorations has since been hijacked by the so-called Marikana Support Group and the programme filled with only opposition political parties," he said.
The commemoration to mark the deaths of 44 people during a wage-related strike at Lonmin's Marikana mines will be held on Friday.
Thirty-four mineworkers were killed on 16 August last year when police fired on them while trying to disperse and disarm them.
Ten people, including two policemen and two security guards, were killed the preceding week.
Lonmin workers went on an unprotected strike for a monthly salary of R12 500.
They gathered at a hill near Nkaneng informal settlement carrying weapons, such as pangas, spears, knobkerries, and iron rods.
Seshoka said the good intentions of Amcu president Joseph Mathunjwa were "muddied" by what he described as the unilateral hijacking of the commemorations.
The NUM initially welcomed Mathunjwa's invitation to its president Senzeni Zokwana to the commemoration.
He asked Zokwana to share the stage with him in an attempt to ease tensions in the platinum belt.
Several violent deaths in the area following the Lonmin strike have been blamed on rivalry between Amcu and the NUM.
Lonmin signed an agreement with Amcu this week, recognising it as the company's majority trade union.
The agreement set a threshold of a 30% membership for any trade union to be recognised by the company.
Membership of the NUM, which used to be the majority union, has dropped to 20% of Lonmin's workforce.
Seshoka said the mining sector had always been a multi-union environment where smaller unions with as little as 3% membership co-existed with the NUM irrespective of its majority.
"The National Union of Mineworkers saw it fit to not be party to these commemorations as well as to desist from organising separate commemorations as these may fuel tensions."
At a news briefing on Tuesday, it emerged that workers had asked Amcu, their legal representatives, the SA Council of Churches (SACC), and the Marikana Support Group to organise the event.
SACC president Bishop Johannes Seoka said the organisers wanted the event to be peaceful and inclusive.