Testifying before the Truth and Reconciliation Commissin, Botha said he had not been involved in the negotiations that led to the release of the six.
"My recollection is that the National Intelligence Serve and/or defence force were involved," he told a TRC panel chaired by commission chairman Archbishop Desmond Tutu.
Asked to comment on allegations that the government paid between US3 million and US22 million for the release, he said: "I can remember that an amount was paid to the Seychelles government but I cannot remember what the amount was.
"The figure I have in my memory is somewhere between US3 million and US6 million."
Botha was testifying on the first day of te TRC's public inquiry into the activities of the now-defunct State Security Council, the body once responsible for the formulation of national security policy.
He said the first he heard of the Seychells coup attempt was when he was woken on the morning of November 26, 1981 by the late Louis Le Grange, then the minister of law and order.
Le Grange told him an Air India aircraft had been hijacked in the Seychelles and was en route to Durban.
"As he was talking, a gut feeling took hold of me that there could be only one reason for hijackers to want the aircraft to land at Durban. They had done something terribly wrong in the Seychelles, and Durban offered them the best chance of escape or survival.
"I responded to my colleague in a way which he considered somewhat insulting. I told him this fuck up would once and for all establish South Africa as the haven for terrorists and pirates."
He said he was later censured by State President PW Botha for his remarks.
Pik Botha denied suggestions that the Seychelles coup was discussed or approved by the cabinet or SSC.
He acknowledged the report of a United Nations Security Council inquiry, which found that the arms, ammunition and other equipment used by the coup plotters were supplied by the SA Defence Force.
The inquiry also found that South Africa's National Intelligence Service had been aware of the coup plans from the start. Members of the SADF Second Reconnaissance Commando took part in the operation.
Botha was asked to comment on an SSC meeting in December 1982, at which president FW de Klerk made a recommendation on the satus of foreign nationals who took part in the Air India plane hijacking and who were acquitted after a trial in Pietermaritzburg.
De Klerk reportedly told the SSC he was against deporting them.
"I vaguely remember that an argument was put forward to the effect that the persons concerned stood trial in South Africa, and if they were acquitted, further action aganst them would be unfair and would amount to punishment meted out by the government," Botha said.