He also denied he made any specific recommendations to former State President F W de Klerk in a situation report on his preliminary investigation into covert activities involving SA Defence Force members.
In a statement in Pretoria, Steyn said he only advised de Klerk to order a criminal investigation after 23 officers had already been suspended or compelled to take early retirement.
The Truth and Reconciliation Commission earlier this week said de Klerk had ignored recommendations by Steyn to investigate claims implicating generals Joffel van der Westhuizen, Kat Liebenberg and Georg Meiring, now chief of the SA National Defence Force, among some 60 military personnel involved in illegal or unauthorised activities.
Commission vice-chairman Alex Boraine told reporters on Thursday that Steyn, then military Chief of Staff, gave the report to de Klerk, and de Klerk had asked Meiring, Liebenberg and van der Westhuizen to tell him which of the names on the list should be retired early or dismissed.
Steyn however said Friday night: "In November 1992, the then State President, F W de Klerk, instructed me to investigate covert activities outside the normal manadate of the SA Defence Force. The primary aim was to focus on activities related to the investigation by the Goldstone Commission.
"With the approval of Mr de Klerk, the former SADF counter-intelligence organisation and the counter-intelligence of the former National Intelligence (Service) were utilised to gather intelligence regarding these covert activities.
"In December 1992, I gave a situation report to Mr de Klerk and selected members of his cabinet, based on my investigations thus far. At this stage I made no specific recommendations, other than to urge Mr de Klerk to act expeditiously," Steyn said.
De Klerk, in consultation with Meiring, Liebenberg and van der Westhuizen, then decided to act against 23 SADF members, Steyn said, adding his notes had been available for this purpose.
"Subsequent to Mr de Klerk's decision, I was instructed to continue my investigation as well as organisational restructuring of the intelligence services of the SADF," Steyn said.
"Given the decision to act against individuals, I then recommended that a criminal investigation be conducted. This was initiated in January 1993 by the Attorneys-General of the Transvaal and Witwatersrand."
Steyn said his involvement in the matter came to an end in July of that year after several further written reports to de Klerk. He retired from the SADF four months later.
"As a professional soldier, I carried out instructions given to me by the former State President."
Steyn said in October 1996 he was invited by the TRC to make a submission.
"I considered it my duty as a committed South African to co-operate with the body. In the interest of national reconciliation and for the Truth Commission to get to as full a picture as possible of our history, I believe it was my duty to co-operate with the commission," he stated.
Later Anton de Klerk, spokesman for Steyn, told Sapa that information given by the TRC - that Steyn had named the generals allegedly implicated or involved in unlawful or unauthorised activities as Joffel van der Westhuizen, Kat Liebenberg and Georg Meiring, now chief of the SA National Defence Force - was untrue.
"He (Steyn) did not point a finger at any of them... never, ever," said de Klerk.
He added that when Steyn made his initial report to then State President, FW de Klerk had routinely informed the generals of its content.
Asked if the TRC comment was then not true on this matter, Anton de Klerk replied: "Definitely."
Professor Charles Villa-Vicencio, the TRC's research director, said in a statement to Sapa on Friday night: "General Steyn said that intelligence indicated that members of components of the SADF were involved in unauthorised and illegal actions. He (Steyn) strongly recommened a criminal investigation in order to substantiate or disprove this intelligence.
"The three generals named were among those whom it was recommended should be investigated to substatiate or disprove the intelligence.
"It was General Steyn's view that the investigation should cover everyone named in his report from the highest to the lowest ranking officer."
SA National Defence Force chief Gen Georg Meiring on Friday denied claims by the Truth and Reconciliation Commission that he and two other army generals had been involved in unauthorised or illegal activities.
"It would appear that to date no substantiation for the allegations could be found," he said in a statement in Pretoria. "No charges have been laid and there were no court appearances."
Meiring said he was arranging a meeting with the commission to discuss the matter.
Meiring added he could confirm that Steyn had conducted an investigation, and that 23 SA Defence Force members were as a result suspended or compelled to retire pending further investigation.
"I am not aware of the 60 names mentioned by the TRC."
In January 1993 Steyn arranged a meeting to bring the accusations to the attention of those who could assist in the investigation, Meiring said.
Those present included Witwatersrand Attorney-General Klaus von Lieres und Wilkau, Transvaal Attorney-General Jan D'Oliveira, Lt-Gen J le Roux from the police, National Intelligence Service official Kobus Scholtz and a representative from the Office of Serious Economic Offences.
Meiring said the SADF had provided the committee with all the information obtained through internal and other probes to enable it to continue its investigation into individuals who had been suspended.
The allegations could not be substantiated.
"On behalf of myself, Gen Liebenberg, Lt-Gen van der Westhuizen, I deny the allegations put forward during the TRC media conference yesterday (Thursday)," Meiring said.
Former State President F W de Klerk on Thursday rejected allegations that he ignored a recommendation by Gen Pierre Steyn in 1992 to investigate claims implicating senior army generals in illegal activities.
These and other allegations in a statement by Truth and Reconciliation Commission vice Chairperson Dr Alex Borraine were misleading, de Klerk said through his spokesman, Fanus Schoeman.
"He is astounded and disappointed that Dr Boraine should have thought fit to launch a public attack on him without first providing him or the National Party an opportunity to discuss the serious insinuations," Schoeman said in a statement in Pretoria.
"The NP must reluctantly conclude that this is a calculated attempt by the commission to harm Mr de Klerk,"he added.
The existence of Steyn's report was confirmed for the first time by the TRC at a media briefing in Cape Town on Thursday.
Boraine said de Klerk had always insisted that a written report did not exist.
Schoeman reacted by rejecting this statement as "seriously misleading".
He said Steyn in 1992 gave de Klerk an oral briefing on his investigation, during which certain papers were handed to the former president. He was also shown a diagram.
"However, he did not retain these documents or even have the opportunity of studying them in depth. He also gained the impression that the document was Lt-Gen Steyn's personal copy, and that he was not intended to take possession of it," Schoeman said.
The document was not an official report to the former State President,he said.
"It was made available to him only insofar as he had it in his hands at some stage of the briefing," Schoeman said. " Mr de Klerk has never denied that he had such documents with him during the briefing."