In July 1940 after the armistice, Auphan became director of the French merchant marine. In September 1941, he was named chief of the general naval staff, a position to which in April 1942 he added that of secretary of the navy in the Vichy government. Auphan's defenders later claimed he only accepted these posts to ensure the fleet's continued freedom from German control.
Both before and after the November 1942 Allied invasion of North Africa, Auphan and former French supreme commander General Maxime Weygand pressed Marshal Henri Pétain, head of the Vichy government, to support the Allies openly. After the Allied landings on 8 November 1942, Auphan and Weygand urged Pétain to accept the North African cease-fire with the Allies that Darlan, then in Algiers, had negotiated. At the insistence of collaborationist Vichy French Premier Pierre Laval, Pétain initially condemned Darlan's negotiated cease-fire, but Auphan persuaded Pétain to reverse this stand. On 10 November 1942, Auphan sent a telegram legitimizing Darlan's accord with U.S. Army Lieutenant General Mark W. Clark. Auphan hoped to arrest Laval, but he could not obtain Pétain's authorization and was the only minister to advocate a cease-fire agreement for all North Africa. On 11 November, Auphan ordered Admiral Jean de Laborde at Toulon to destroy the French fleet should German forces threaten the port. With Pétain's approval, on 13 November Auphan cabled Resident General Charles Nogu?s of Morocco to transfer to Darlan command of all North Africa. On 18 November, Auphan resigned to protest Laval's assumption of full governmental powers.
On 18 August 1944, Pétain empowered Auphan to negotiate the transfer of power to the Free French leader Charles de Gaulle, a development that de Gaulle completely ignored. In September 1944, the new French government revoked Auphan's pension, and in August 1946 the French High Court sentenced him to lifetime imprisonment and forced labor for treason, including for having commanded the Toulon fleet's destruction. Released in January 1955, Auphan was rehabilitated in November 1956. He subsequently published extensively in naval and political history. Auphan died at Versailles (Yvelines) on 6 April 1982.
Auphan, Paul, and Jacques Mordal. The French Navy in World War II. Trans. A. C. J. Short. Annapolis, MD: Naval Institute Press, 1959.; Auphan, Paul. Les Grimaces de l'histoire suivies de l'histoire de mes trahisons. Paris: Les Iles d'Or, 1951.; Auphan, Paul. Histoire élémentaire de Vichy. Paris: Éditions France-Empire, 1971.; Auphan, Paul. L'Honneur de servir: mémoires. Paris: Éditions France-Empire, 1978.; Paxton, Robert O. Parades and Politics at Vichy: The French Officer Corps under Marshal Pétain. Princeton, NJ: Princeton University Press, 1966.