Pagad leader Abdus-Salaam Ebrahim on Wednesday claimed in court that former Vlakplaas commander and NIA agent Dirk Coetzee and security company boss Cyril Beeka were behind a bombing at the Waterfront.
In his bail application in the Cape Town Regional Court, Ebrahim - who is accused of the murder of former Hard Livings gang boss Rashaad Staggie, the attempted murder of former Pagad leader Ali Parker and intimidation and extortion - also claimed NIA members had killed police Pagad investigator Bennie Lategan.
Lategan was ambushed and shot dead by gunmen at the intersection of the R300 highway and Vanguard Drive early last year.
Beeka, the boss of a security company, is on trial for the murder of a Chinese national.
Ebrahim said Paul Eia, a lawyer who had represented Pagad members previously, had phoned him to arrange a meeting after having coffee with prosecutor Willie Viljoen.
"I received a call from him and he sounded quite upset. I went to see him at his chambers and he informed me that Viljoen had had coffee with him that morning. He said Viljoen had told him Lategan was killed by the NIA because he had stumbled on to things that linked the NIA to urban terrorism.
"He said Mr Viljoen had told him the information they had was that Cyril Beeka and Dirk Coetzee were responsible for the Waterfront bomb because they wanted to control the security network in the area," said Ebrahim.
Ebrahim did not specify which of the two bombs at the Waterfront he was referring to, the August 1998 pipebomb at Planet Hollywood or the New Year's Day pipebomb in a car park at the Waterfront.
Viljoen, of the Investigative Directorate of Organised Crime, said these allegations originated with former Pagad Gauteng co-ordinator and NIA informer Ayob Mungalee and Ebrahim.
He told the court he had approached Ebrahim in the High Court in the presence of his legal representative and said that if he had any evidence of his allegations he should bring it forward, because he wanted to investigate independently.
Viljoen asked Ebrahim on Wednesday why he had not shared any of the information.
Ebrahim had replied: "There is information, but we cannot give it unless there is someone we can trust. We don't know who to trust at the moment.
"We need a government official who can look at it critically, without prejudice. Otherwise, it can be used unjustly or be destroyed."
Captain Heinrich Cooper, investigating the murder cases of Staggie, Farouk Jaffer and Adam and Faizel Vinoos, dismissed the allegations of NIA involvement in Lategan's murder.
He said the allegations originated as a misunderstanding from a source whose information turned out to be negative.
"A vehicle similar to the one used in Bennie Lategan's ambush was earlier seen at the funeral of Yusuf Jacobs (a Pagad medic)," he said.
He said witnesses could place Pagad members at the scene.
Cooper also said he had witnesses's statements and video footage placing Ebrahim at the scene of Staggie's murder in 1996.
"In the video made when Staggie was killed, it was clear that the accused had a clear role from the start at Gatesville Mosque to Staggie's house and he was one of those persons who tried to drag Staggie out of his vehicle.
"The accused was inside and outside the mosque with a shotgun and about seven shotgun shells were found at the scene of Staggie's killing. These were later linked to the accused's shotgun," said Cooper.
Witnesses were only prepared to testify if Ebrahim was denied bail, he said.
He then linked Ebrahim to a wide range of cases, including the attempted murder of Parker and Jaffer, and claimed he had evidence that Ebrahim tried to interfere with witnesses in Pagad member Ebrahim Jeneker's trial.
Cooper said: "Mr Parker had made a statement that he was called a traitor and an enemy of Allah, and he has given a description of the person who attacked him which fitted the profile of Mr Ebrahim."
Ebrahim was also the man who had ordered attacks on Americans drug dealer Kadika Madat's Tafelsig home.
Cooper said he had a record of cellphone calls made between Pagad member Abzhal Karriem and Ebrahim on the night and a week before Jaffer's murder.
Karriem has been charged with Jaffer's murder.
The bail application resumes today.