The document also said the military massacred civilians in South Africa to stir ethnic tensions, according to the so-called "Steyn report" published for the first time Friday in the Weekly Mail and Guardian.
Leaders of the former government denied the existence of the report and kept it under wraps for five years.
The document is based on a 1992 investigation by former defence chief of staff General Pierre Steyn into claims of a covert "third force" operating within the apartheid army.
According to a synopsis of the report obtained by the weekly, Steyn found that the army secretly stockpiled arms in Kenya, Zambia, Mauritius and other, unidentified, countries to be used by Pretoria's special forces to destabilise those states, as well as a new, black-led government in this country.
Arms were also stored in game reserves in South Africa, the report says.
It confirms that military agents armed and trained Mozambique's RENAMO rebels, as well as Zulu nationalist Inkatha Freedom Party (IFP) militia in KwaZulu-Natal province in the early 1990s - long after the government said it had stopped supporting these groups.
Steyn found that army agents, with the help of the state-owned railway corporation, were involved in a spate of massacres on Johannesburg commuter trains in the early 1990s.
At the time, the white government blamed the almost weekly attacks on feuding between Nelson Mandela's African National Congress and the IFP.
Former president Frederik de Klerk, who commissioned the probe, had said that Steyn briefed him verbally on his findings, but never submitted a written report.
The Truth and Reconciliation Commission investigating apartheid-era human rights abuses earlier this month announced, however, that it had acquired a written version of the report and said it was looking into the charges it contains.
The Mail and Guardian said the report was considered so "explosive" that even Mandela, briefed on its contents after becoming president in 1994, chose to conceal it for two years lest it disrupt the country's delicate political transiton.
The truth commission, led by Nobel peace prize laureate Desmond Tutu, revealed that the reported implicated three top officers, including current defence force chief Georg Meiring, in political "dirty tricks," but that De Klerk took no action against them.