On his return from Europe in 1910, Basedow entered the geological department of South Australia as Assistant Government Geologist. He resigned from this position in 1911 to take up the newly created Australian federal government position of Chief Medical Officer and Chief Protector of Aborigines in the Northern Territory. He arrived in Darwin on 17 July 1911 and left 45 days later unhappy with his working conditions and claiming the legislation under which he was operating was unworkable. Basedow returned to Adelaide and set up in medical practice, combining this with consulting geological investigations for individuals and organisations. He continued to publish in learned journals, mainly on anthropology but also on geology.