The former South African defence force surgeon-general, 63, now risks being barred from practising medicine after the council ruled that he had flouted ethical rules.
Basson faced charges over supplying suicide cyanide capsules to operational officers, tranquilising substances for kidnappings, and for producing sedatives, ecstasy and tear gas.
"The breaches of medical ethics amount to unprofessional conduct," said Jannie Hugo, chair of a Health Professions Council of South Africa (HPCSA) committee on the matter.
The charges stem from Basson's time working for the white minority state's chemical and biological warfare programme in the 1980s and early 1990s.
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In October 1999, he appeared in the Pretoria High Court facing 67 charges against him, including murder, fraud and drug trafficking.
The trial lasted two-and-a-half years and depicted Basson -- nicknamed Dr Death by the national media -- as the mastermind of a secretive chemical and biological weapons programme dubbed Project Coast.
Basson allegedly oversaw plans to poison Namibian fighters with muscle relaxants, infect water with cholera, and deliver a baboon foetus to intimidate Nobel Peace Prize winner archbishop emeritus Desmond Tutu.
He was acquitted of the charges in 2002, and today runs a profitable cardiology business in Cape Town.