When the war began on 1 September 1939, Mutschmann was appointed the Reich Defense Commissioner for Wehrkreis (Military District) IV that included his Gau as well as Gau Halle-Merseburg, northern Reichsgau Sudetenland and part of Gau Thuringia. On 16 November 1942, the jurisdiction of the Reich Defense Commissioners was changed from the Wehrkreis to the Gau level, and he remained Commissioner only for Gau Saxony. As such, Mutschmann had responsibility for air and civil defense measures and was blamed for not adequately preparing for the horrific bombing of Dresden which occurred from 13-15 February 1945.