It asked anyone who had been treated by Dr Gupta since January 26 to contact the ministry.
Dr Gupta formerly worked in the ophthalmology department at Dunedin Hospital, but did not treat any patients for the Southern District Health Board after being deregistered.
Dr Gupta is understood to have registered with the Wakaminenga Kaunihera Hauora Health Council (WKH), an organisation which claims to be able to register medical practitioners under "sovereign native customary ture tikanga".
The Medical Council is the only organisation in New Zealand legally able to register medical practitioners.
Medical Council chairman Curtis Walker said his organisation had no association with WKH, and said the council ensured all practising doctors met and maintained minimum standards of competence and fitness to practice.
The Ministry of Health is understood to be aware of WKH and to be considering what to do about the organisation.