General Johan van der Merwe, subpoenaed by the Truth and Reconciliation Commission (TRC), said that Adrian Vlok, the former law and order minister, instructed him to destroy Khotse House in 1988 and said the order came from Mr Botha.
Yesterday's revelation takes the commission, set up to uncover the truth about the apartheid years, closer than ever before to the old National Party cabinet and to Mr Botha. It now looks increasingly likely that the former president will be subpoenaed to appear before the TRC. A few weeks ago, Mr Vlok became the first minister to be called.
Such a subpoena would be politically delicate and socially divisive. Mr Botha refuses to recognise the commission.
Yesterday's evidence undermines assertions by Mr Botha's successor, FW de Klerk, during his party's official submission to the TRC in the summer, that while the National Party created the conditions under which atrocities could take place, it never ordered them. Mr Botha did not co-operate with the party's submission.
General van der Merve's revelation took yesterday's TRC hearing in Johannesburg by surprise. He had been called to give evidence in support of five police officers seeking amnesty for an array of apartheid-era atrocities in return for information on 40 killings, including high-profile political assassinations. The five - including Brigadier Jack Cronje, former commander of the notorious Vlakplaas hit squad - are the most senior police officers to approach the commission.
Lawyers claimed before the hearing that their clients would implicate senior officers, former ministers and even provide ammunition for the TRC to subpoena Mr Botha. Further allegations concerning the former president are expected during the week-long hearing.
At the opening of the hearing the men called on their superior officers and National Party leaders to admit authorising illegal acts to keep themselves in power. In a statement they said they found it hard to believe Mr de Klerk's assertion that he had been unaware of government-authorised assassinations, tortures and rapes.
Extracts from a 1917 speech by General Jan Smuts and a poem by Afrikaans poet C Louis Leipoldt set the emotional atmosphere as the men claimed they were not criminals but had always acted in the interests of the National Party and their country. They said they had been misguided but were brought up to believe apartheid was sanctioned by God through the church and that black people were inferior. The men must convince the commission that their acts were politically motivated to win amnesty.
The start of yesterday's hearing was held up by the increasingly bitter battle between the commission and state prosecutors concerning authority over alleged perpetrators of apartheid crimes and witnesses in pending criminal prosecutions.
The submission for amnesty by the five police officers was a coup for the TRC which has been criticised for failing to flush out perpetrators. The last seven months of hearings have focused on victims' harrowing stories. But last week, when the commission announced the names of the five men who would testify, Jan D'Oliviera , Transvaal attorney general, had two of them arrested and charged with murder in connection with a two-year investigation. Yesterday, he opposed subpoenas on four police officers, who are witnesses in pending criminal cases, to this week's commission hearings. The commission reserved judgment on Mr D'Oliviera's objections.
The courts complain that the TRC is interfering with long-running investigations. Two weeks ago the commission complained that the courts were the wrong forum for South Africa to deal with its apartheid past following the state's failure to convict General Magnus Malan and other generals of 13 murders, despite a seven-month trial costing 7 million rand (pounds 1m).
In a separate development yesterday an official submission to the TRC by the South African National Defence Force denied that thousands of compromising military documents from the apartheid era had been destroyed by the military. General George Meiring, head of the SANDF, said told the commission that he was not aware of any unauthorised or illegal destruction of documents.
acknowledged in testimony to the commission that apartheid-era files had been destroyed to protect covert activities by the force.