In June 1945 Jones was promoted Acting-Captain RNR and posted to South East Asia Command under Admiral Mountbatten. He was appointed as divisional sea transport officer of the Netherlands East Indies, based in Java, Batavia. The war in Asia had ended in August 1945 with the Japanese capitulation but they were still required to deal with the return transport of troops and supplies, as well as the shipping of the civilian and military prisoners of war out of the Japanese camps.