 Shortly after the outbreak of World War II, on 1 December 1939, Jones was raised to temporary group captain.In March 1940, he returned to the position of Director of Training and assumed responsibility for Australia's part in the Empire Air Training Scheme (EATS), establishing many schools, acquiring hundreds of aircraft, and overseeing the training of thousands of airmen.The RAAF's Central Flying School was reformed in April 1940 to meet the vital requirement for additional flying instructors, whose numbers would grow from 16 in the first year of the war to 3,600 by 1945.