Dr J. Stokes Millner left Adelaide for Port Darwin on the Kohinoor on 17 December 1869 and arrived on 21 January 1870. Here he became Acting Government Resident, Medical Officer and Protector of Aborigines at a salary of 500 pounds per annum. Millner was also required to keep meteorological records, collect indiginous plants and aquire some knowledge of the languages of the Aboriginal tribes as soon as possible and make them understand that they were British subjects.
While there he became involved in the gold mining industry and worked a gold claim with Captain Bloomfield Douglas. For a while he also read services in Barclay's Room on Sundays until the arrival of the Rev J.A. Bogle.
When Bloomfield Douglas was appointed Government Resident in April 1870, Millner resumed his medical practice with Edward Rix as assistant.
He left for Adelaide in 1875 on the Guthenburg which was wrecked on a reef during a storm near Flinders Passage. Of the 99 passengers and 38 crew only 22 survived. Millner was not one of them.