A register of medical practitioners was first required to be kept in 1838 in New South Wales and was published in the Government Gazette each year. The New South Wales gazette is now freely available to search online.
The Australian Medical Pioneers Index provides biographical data on over 4500 doctors who lived in Australia or visited Australian shores in a medical capacity in colonial days until 1875.
The State Records of NSW also has an excellent guide to Medical Practitioners.
The State Library of New South Wales holds a significant collection of material related to Doctors that could assist you with researching your medical practitioner ancestor.
We also have the The Australasian medical directory and hand-book from 1883 and a CD-ROM called Australasian Medical Directory Compendium which includes facsimiles of some early medical directories.
Ancestry Library which the State Library of NSW offers as an onsite database also includes some UK medical registers such as UK Medical Registers, 1859-1959 and UK & Ireland, Medical Directories, 1845-1942.