In 1943, Clunies Ross was appointed Director of Scientific Personnel in the Commonwealth Directorate of Manpower and also Adviser on the Pastoral Industry to the Department of War Organization of Industry. He held these positions until 1945 while continuing work connected with his university position. At the end of the war he left the university to assist the CSIR in planning
sheep and
wool-textile research. In 1946 he was appointed a full-time member of the CSIR Executive Committee, which was situated in
Melbourne. He served as the executive officer of the CSIR until 1949 when it was renamed the CSIRO. He was chairman of the CSIRO until his death in 1959. During this time he oversaw the release of
myxomatosis for
rabbit control in
Australia. In his retirement he was president of the Melbourne
Wallaby Club 1954 – 1955. While in his role at the CSIRO Clunies Ross came into conflict with pioneering radio astronomer
Ruby Payne-Scott over the role of women in the organization, and her role in particular. The two met in person to discuss the disparity in pay and working conditions between male and female employees of CSIRO, but this did not result in change to the status quo. When Payne-Scott's marriage and pregnancy were revealed, the two had a hostile exchange of letters, and CSIRO consequently deprived her of permanent employee status and pension funds. ==Later years and legacy==