Tutu, reacting to an interview with Rapport in which Botha said he would rather be taken to court and charged because he was not prepared to appear before the TRC, said if that was the case the law would take its course.
"I am very sad at the way in which Mr PW Botha has appeared almost to have thrown down a gauntlet to the TRC in a newspaper interview published today," Tutu said in a statement.
"Since I travelled to George to have discussions with Mr Botha a year ago, the commission has gone out of its way to be accommodating to him in view of his age, his health and his position as a former state president."
Tutu said the commission waited since the beginning of the year for answers to questions which it submitted to Botha in accordance with an agreement made with him last year. "We now understand we will have those answers shortly, but we have constantly extended the deadline for the answers," he said.
He said the TRC made special representations to the government to enable Botha to have the necessary legal assistance in order to provide the necessary answers.
The TRC also proposed a special hearing to accommodate Botha after his representatives indicated that he was not well enough to travel to Johannesburg last month to attend the hearing on the role of the former State Security Council.
"In the same way as I was prepared last year to travel to see Mr Botha, we are prepared to hold the second round of our State Security Council hearing in George, close to his retirement home," Tutu said.
"In showing this consideration for Mr Botha, we have angered many South Africans who have accused us of being spineless for not unceremoniously calling him to account."
The commission would proceed in the normal way with the organisation of the second round of the SSC hearing, Tutu said.
The Promotion of National Unity and Reconciliation Act required transparency of the commission and such a hearing had to be held in public - in the absence of compelling reasons laid down in the Act which would require it to be closed.
"A hearing cannot therefore be replaced by private talks between Mr Botha and myself," Tutu said.
"A subpoena was issued for Mr Botha to appear at the first SSC hearing and it would be odd in the extreme for us to withdraw it for the second. Other former Cabinet members have appeared under subpoena, as have people as prominent as Mrs Winnie Madikizela-Mandela. We very much hope Mr Botha will agree to attend but if he does not, the process will take its course."
Although Tutu did not elaborate on this, it is understood that the next step will be for the commission to decide whether to lay a charge against Botha in terms of the Promotion of National Unity and Reconcilaiton Act.
The Act says that if anyone who has been subpoenaed does not appear before the commission, without sufficent cause, he or she faces a fine, up to two years' jail, or both.