In July 1940 he was appointed to command of RAF Leeming, Yorkshire. On 1 December 1940 he was promoted to temporary group captain, and in January 1941 appointed an Air Aide-de-Camp to the King. His next assignment was as Senior Air Staff Officer, Headquarters RAF Far East, in July 1941, being promoted in January 1942 to acting air commodore, and on 11 February was assigned as Senior Air Staff Officer, Westgroup, Java. On 10 March 1942, following the Battle of Java, he was taken prisoner. Staton would spend the remainder of the war as a prisoner of the Japanese, and would undergo torture for refusing to disclose information to them. To punish him for his holding out against questioning, Japanese interrogators removed his back teeth. Staton proved an uncooperative prisoner and was moved sixteen times, spending time in camps in Batavia, Singapore, Japan, Formosa, the Gobi Desert, Mukden, and Siam. On 8 October 1943, while a prisoner, his temporary rank of group captain was made war substantive. Staton was released from captivity in September 1945 after three and a half years as a POW. Later he submitted written evidence to prosecutors at the War Crimes Trial of three Japanese officers from camps in Formosa.