Kahn told a news conoference that throughout the consideration of this matter, Botha's personal circumstances had weighed heavily on him.
"He is almost 82 years of age and no attorney-general in any civilised country lightly decides to prosecute a person of his age, especially given Mr Botha's medical history."
Kahn said he had considered all the circumstances, including the voluminous documents upon which the TRC wished to question Botha at a public hearing, and had decided that a prosecution was warranted in law and in the public interest.
Botha would accordingly be charged in the George Regional Court. He would be summonsed to appear on January 23.
Kahn added that the TRC had decided not to press charges in relation to media references to its standing, and there would be no further charges.
Botha was subpoenaed to appear before the TRC on December 19 but failed to turn up after saying earlier that he did not intend to appear.
Botha has called the Truth Commission a circus and a witch hunt against apartheid leaders, and said repeatedly he would not testify. He failed to appear before the commission three times.
TRC chairman Archbishop Desmond Tutu asked that Botha be charged because he refused to appear before the commission.
Earlier, Botha's lawyers delivered 1,700 pages of documents tot he TRC in which the former president denied knowledge of killings, torture or bombings carried out by security forces.
Earlier this month Kahn said that Botha had undertaken to obey any summons issued under the Criminal Procedures Act. The summons would give Botha 14 days' notice to appear in court.
Botha faces a possible two years in prison or a fine of R20000 if convicted on the main charge of failing to appear before the TRC.
The alternative charge is hindering the commission in the execution of its duties.