The defence ministry inquiry is one of several into links between the Swiss and South African secret services during the apartheid era.
This probe centred around allegations that the former head of the Swiss secret service, Peter Regli, helped the apartheid regime secure illegal drugs intended for crowd control.
The probe was initiated after the former boss of South Africa's chemical and biological weapons (CBW) programme, Wouter Basson, implicated Regli during his trial testimony.
On the witness stand, Basson - nicknamed "Dr Death" - alleged that Regli had brokered an arms and drug deal with corrupt Croatian officials.
Basson said Regli was trying to buy enriched uranium from the Croatians and, as part of the deal, he had helped Basson to secure 500 kilograms of methaqualone (also known as Mandrax), which Basson brought to South Africa in 1992.
For his part, Regli denied any involvement in such a deal. During the trial, he described Basson's allegations as "unsubstantiated slander" and a sweeping defence by a criminal".
In an interview shortly after Basson made the allegations, Regli told swissinfo that Basson's contacts with the Swiss secret service had been confined to a Swiss reserve officer who was involved in intelligence at a "technical level" in South Africa.
He added that this officer had "nothing to do with the strategic intelligence where I was director".
The reserve officer in question was a Swiss arms dealer, Jürg Jacomet, who Basson said introduced him to Regli. Jacomet has since died.
An earlier parliamentary inquiry, which wound up in 1999, found that Regli's contacts with the South African secret services were "purely of an informative nature", and cleared him of any involvement in South Africa's CBW programme.
However, Basson's testimony led to calls for a new probe, which the defence ministry set in motion last year.
The probe is one of four currently underway into Switzerland's links with the Apartheid regime. One is being conducted by the Federal Prosecutor's Office, another by a standing parliamentary committee, which is also looking into links between the two secret services.
A more general inquiry, set up in May 2000, is analysing Switzerland's relationship with apartheid-era South Africa.
Run by the National Science Foundation, it warned recently that problems with gaining access to companies' archives were severely impeding its work. The team of 40 researchers, under historian, Georg Kreis, has so far come up with nothing (see telated story).
During Basson's trial, South African media gave little credence to his allegations, pointing out that he had made them while defending himself against fraud - one of 67 charges levelled against him during his two-year trial.
Basson was acquitted of all charges - including trafficking in drugs, fraud, murder and conspiracy to murder - earlier this year.
He headed South Africa's CBW programme - dubbed Project Coast - from 1981 to 1993, when it was closed down shortly before the country's first democratic elections.