Following the outbreak of war with Japan, Allen returned to Australia in March 1942, and in August took charge of operations against the Japanese advance along the Kokoda Track. Although he was successful, Allen nevertheless came under what many consider unfair criticism from the Allied commander in the South West Pacific Area, U.S. General Douglas MacArthur and the Allied land forces commander, the Australian General Sir Thomas Blamey, for moving too slowly in pursuit of the Japanese across the Owen Stanley Ranges. He was relieved of his command on 29 October 1942. Lesser appointments followed, but in October 1944, Blamey recommended Allen be made a Knight Commander of the Order of the British Empire, although Allen was never appointed.