Barnard, and his successor as NIS head Michael James Louw, filed the application concerning the Truth and Reconciliation Commission's final report in the Cape High Court on Friday on behalf of all former NIS operatives - to clear their names, it was claimed.
The TRC report held the operatives accountable for extra-judicial killings on the grounds that information they gathered was used to eliminate political opponents.
Barnard, NIS head between June 1980 and January 1992, said he had been grouped with the likes of Eugene de Kock, Joe Mamasela and Dirk Coetzee despite being held in high esteem by his colleagues and those who initially saw him as an enemy.
He said the application was urgent because the TRC had a limited lifespan. The TRC has 14 days to produce its records. A hearing is unlikely before next year.
Barnard said in the application that the TRC's findings reflected seriously on his reputation and had led to calls for his resignation.
"In my view, the incumbent of a position such as mine must be above suspicion. It would therefore be in the interests of the province itself and its inhabitants if the blot on my reputation could be removed as a matter of urgency," Barnard said.
Describing his role in the former government, Barnard said it was a matter of public record that preparations he was intimately involved with from the start culminated in talks between the African National Congress and the South African government.
Barnard said he engineered the first meeting between President Nelson Mandela and former state president PW Botha.
He had also been involved in peace brokering as NIS head, including in the normalisation of relations with Mozambique which resulted in the Nkomati Accord, the independence of Namibia and the resolution of the Angolan conflict, and the development of Africa's capacity to defuse conflicts on the continent.
He said many heads of state he had negotiated with over the years were still in office, and his counterparts in the intelligence community understood and appreciated his role and involvement in the transition.
Barnard, describing a difference in approach between the NIS and the SA Defence Force, said the SADF had manipulated security intelligence to enlarge its claim on South Africa's human and financial resources.
The NIS, on the other hand, had argued for a peaceful resolution to South Africa's problems, and said it was in the country's security interests to allocate resources to socio-economic upliftment.
He said the NIS' fundamental position was that the country's problems and dangers could be effectively addressed only by radically changing the political status quo.
Against this background, the TRC's findings implicating the NIS and himself in extra-judicial killings caused immeasurable personal harm, Barnard said.