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"In the light of all the circumstances, the breaches amount to unprofessional conduct... the respondent is guilty of unprofessional conduct," HPCSA professional conduct committee chairman Prof Jannie Hugo said in Pretoria.
Basson had presented nine arguments at an inquiry into his conduct in which he claimed he acted as a soldier and not a doctor, and that he was not aware of the ethics.
Hugo said Basson contravened international protocols and conventions. These were the Geneva Declaration of 1948 and the UN convention on the prohibition of and stockpiling of dangerous weapons.
"The respondent confused ethics of a doctor with that of a soldier while discharging his duties. A doctor cannot rely on military orders to escape the consequences of his duties."
Hugo said if a doctor decided to use his medical knowledge and skills and consequently contravene medical ethics, he should deregister as a medical practitioner.
The six-year-long inquiry related to Basson's involvement in Project Coast, between the 1980s and early 1990s.
Basson was accused of acting unethically by being involved in the large-scale production of Mandrax, cocaine and teargas, of weaponising teargas, and of supplying it to Angola's Unita leader Jonas Savimbi.
He is also accused of acting unethically by providing disorientating substances for cross-border kidnappings and making cyanide capsules available for distribution to operatives for use in committing suicide.
In 2002, Basson was acquitted by the High Court in Pretoria of criminal charges arising from his conduct.
The HPCSA reviewed the judgment to establish if there were grounds to continue with an inquiry.
The State appealed against the decision in the Supreme Court of Appeal, but the appeal was dismissed. The State then went to the Constitutional Court but it was dismissed in September 2005.
Sentencing would take place on February 20 and 21 next year.