The report cleared the former head of Switzerland's secret service, Peter Regli, of involvement in South Africa's chemical and biological weapons programme.
However, it did criticise his conduct and his links to the apartheid intelligence services.
In an interview with swissinfo, Regli said he was pleased the long-running saga had finally come to an end.
But he said it was clear that the professor who headed the inquiry, Rainer Schweizer, did not understand the functioning and the rules of an intelligence service.
Peter Regli: I'm basically very happy that the major accusations that have been formulated last year in a heavy media campaign have been disproved. And the fact that the Swiss intelligence service and its director, who I was, [were cleared over allegations that we] participated in the secret South African chemical biological warfare programme.
Second, that there never was a secret agreement between Switzerland and South Africa concerning chemical warfare.
And third, and this is more a national question, that the two Soviet missiles that we bought in the 1990s have been bought in an absolute regular way that I, as a director, didn't do it behind my superiors' backs.
swissinfo: The report says your links with Basson were too close - how close were you?
I have been under inquiry for three years, and my intention is not to support another inquiry by [Swiss] radio. The professor who conducted this inquiry did not understand the functioning and the rules of an intelligence service.
The report said several documents had been destroyed by intelligence services. What's your response?
Intelligence documents that have been evaluated, that have been used and that are not of any use any more have to be destroyed because they belong to the partner. We follow these rules but unfortunately this has not been understood.
Don't you feel that cooperating so closely with the apartheid regime's intelligence services was inappropriate?
I'm basically a democrat as a Swiss and I care very much about the democratic rules in a country.
Second, in Switzerland we were very much dependent on contact with different intelligence services and it was not the task of the director to make any political assessment of yes or no should we be in touch with them or not.
But you described yourself as a "minister for foreign affairs on military and security issues"?
We have a basic mission given by the politicians and the director of the intelligence service has to fulfil this mission. He has to take initiatives and if he does not, he does not fulfil his task.