Recovering from his illnesses he was appointed liaison officer at 6th Division headquarters in September 1943 and was promoted to temporary major that month, which became substantive in May 1945. He later attended the Staff School at Cabarlah, Queensland, and after completing the course he was posted to the 1st Australian Combined Operations Section in October 1944. He was attached to the 7th Division's headquarters and helped plan the amphibious landings at Morotai and Balikpapan. Ferguson was Mentioned in Despatches for his planning.