He said Madikizela-Mandela was not the only ANC leader to appear before the TRC, as several others did, including himself, for kidnapping a police officer during the heydays of apartheid.
Mufamadi says he knew there was an investigation but the orders didn't come from him.
Mufamadi shot down a version of events in the documentary told by the then head of the murder and robbery squad, Henk Heslinga. "Why was that relevant to him?" asked Mufamadi.
Sepei was killed in 1989 at the age of 14 after being accused of being a police informant and his body was found near Madikizela-Mandela's home in Soweto.
Former Police Commissioner, George Fivas also revealed that there was no evidence linking Madikizela-Mandela to the murder.
"There was not a single piece of informationthat fingered Winnie to say she was responsible, maybe personally responsible, for the murder that she gave instructions for Stompie to be eliminated", Fivaz said.
A screengrab shows the documentary "Winnie", based on Winnie Madikizela-Mandela.
He also said he received a call from the EFF commander-in-chief, Julius Malema, last night where Malema told him that when he addresses the claims in the documentary during his briefing, he should do it in such a way that it doesn't cause more fighting.
The director of the controversial documentary Winnie has apologised to former safety and security minister Sydney Mufamadi for failing to give him the right of reply but insists she's proud of her work.
Mufamadi ended the brief by saying: "I still maintain that those of us who fought for the liberation of this country alongside Comrade Winnie are the authorities of what happened. That is really the message I wanted to convey to the people of South Africa".