The commission's findings, made public on Tuesday, demonstrated that national prosecutions head Bulelani Ngcuka "probably never" acted as an agent for the apartheid government.
The commission was set up by President Thabo Mbeki last year after allegations against Ngcuka first surfaced in a City Press newspaper report.
It turned out to have been based on a probe done by African National Congress intelligence structures in 1989 and 1990, which found he may have been police Agent RS452.
The ANC investigation was led by Ngcuka's other main accuser - Mo Shaik, now a foreign affairs department official.
Maharaj also supported the allegations.
"I am happy that the report and its findings have been accepted by President Mbeki and that the report has been made public," Maharaj said yesterday night.
"From the outset I had indicated I would co-operate with the commission. I have done so and the report acknowledges that".
Maharaj had also complained about the leaking of information to media from Ngcuka's office on a criminal investigation into Maharaj and his wife.
He said that since February 14, "I and my family have been tried in the public arena through leaks of Ngcuka's office".
Hefer did not make a finding on claims that Ngcuka had abused his official powers, saying he had been precluded from doing so by the commission's terms of reference.
But he said it was clear there had been leaks from the prosecuting authority about an ongoing criminal investigation into Maharaj and his wife's finances.
"Such a state of affairs cannot be tolerated," Hefer's report states.
In a letter to the judge, Mbeki accepted his main findings and said the information leak would be "followed up". – Sapa.
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