Mafart was a DGSE agent and deputy commander of the French Navy Training Centre in Corsica. He supported the sabotage team that travelled to New Zealand and bombed and sank the Rainbow Warrior, drowning photographer Fernando Pereira.
He was apprehended by New Zealand police, pleaded guilty to manslaughter and was sentenced to 10 years imprisonment on 22 November 1985. Following heavy political pressure from France and her allies and a United Nations-sponsored mediation between New Zealand and France in July 1986, Mafart was deported to the island of Hao in French Polynesia to serve three years. In return, France apologised to New Zealand and paid New Zealand $6.5 million.
However, on 14 December 1987, Mafart was returned to Paris after complaining of stomach pains. After treatment he was not returned to the island and in 1988 enrolled on a two-year course at the École de Guerre (War College) in Paris.
Mafart was promoted to colonel in December 1993. According to Le Monde, Mafart was then serving near Paris on a base housing several command staffs, including that of military intelligence.
His commanding officer during the Rainbow Warrior affair became an aide to Defence Minister Francois Léotard.
He wrote a book "Carnets secrets d'un nageur de combat: Du Rainbow Warrior aux glaces de l'Arctique" (Secret notebooks of a naval frogman: from the Rainbow Warrior to the Arctic ices) that concerned his role in the bombing.