Shyam Acharya is accused of stealing a doctor's name and qualifications in India before moving to Australia.
He used the credentials to work in local hospitals between 2003 and 2014, New South Wales (NSW) Health said. He also became an Australian citizen.
Mr Acharya was never the individual subject of a complaint.
He is facing a fine of up to A$30,000 (Â£18,600; $18,700) but is likely to have left Australia, said NSW Health Minister Brad Hazzard on Wednesday.
"It is quite disturbing that a foreign national could get through our border protection with a false passport and ID based on an Indian citizen who had trained as a doctor," Mr Hazzard said in a statement.
Local media reported the false identity was that of Sarang Chitale, a doctor who had previously worked in India.
The Australian Health Practitioner Regulation Agency (AHPRA) notified NSW Health it was investigating Mr Acharya in November last year.
He worked at four New South Wales (NSW) public hospitals - two in Sydney, and two on the state's central coast - before his employment ended in 2014.
NSW Health deputy secretary Karen Crawshaw said he was classified as a junior doctor, meaning he was supervised by other practitioners.
Although never the sole target of a complaint, Mr Acharya was part of a clinical team investigated over the treatment of one patient.
Mr Hazzard said he would offer to meet with the patient, who had been told of the alleged deception.
Australian police and immigration officials are investigating how Mr Acharya was awarded citizenship.
"The belief is that he actually trained in a medical course, possibly in India," Mr Hazzard told the Australian Broadcasting Corp.
"Whether he actually completed that qualification is a moot point."
NSW Health said the registration process for doctors had undergone significant changes since 2003.
Mr Hazzard said he would examine "every aspect of registration" to prevent any future breaches.
A man who allegedly masqueraded as a doctor in Australian hospitals for over a decade is believed to have left the country, authorities have said.