Health Minister Jonathan Coleman said in a press release last night the patient was being transported from their home to Christchurch Hospital by Iso-pod, where they would be cared for in a special isolation facility.
No details were available last night on who the patient was, or where they were from.
The press release said the patient had reported to the local Public Health Officer.
Otago-Southland medical officer of health Dr Marion Poore, of Dunedin, referred the Otago Daily Times to the Southern District Health Board communications department.
Nobody could be reached late last night.
Mr Coleman said blood samples would be sent to a high-security reference laboratory in Melbourne for testing, with a result expected in between 24 and 48 hours.
The patient had recently been in Sierra Leone as part of New Zealand's contribution to the international response to Ebola, he said.
Gore woman Bronnie McBain recently returned from Sierra Leone, where she worked as part of a medical team in the Ebola-affected country.
She told the ODT last night she did not know who the patient was, and was under a 21-day contractual agreement not to talk to media, having returned to New Zealand within that time.
Mrs McBain directed the newspaper to Ministry of Health guidelines for people returning from Ebola-affected areas.
Those guidelines state that on arrival in New Zealand they will be isolated, and health protection officers contacted to undertake a health assessment and provide advice.
The person would continue to self-monitor at an agreed location in New Zealand until they had completed a 21-day monitoring period.
An SDHB report late last year noted the Ministry of Health was procuring Iso-pods to transport highly infectious cases by air on a retrieval basis, using military aircraft.
Mr Coleman said since returning home to New Zealand, the patient had become unwell.
''Based on the patient's symptoms, the Ebola virus needs to be ruled out.''
Mr Coleman said.
''I am advised that it is quite possible they are suffering from gastroenteritis or some other illness such as malaria. The only person who has been in direct contact with the patient during the potentially infectious period has been the patient's partner.''
The partner was being monitored according to internationally recognised protocols.
New Zealand was well placed to respond to a patient needing to be tested to rule out Ebola.
''Ebola is not easy to catch - transmission requires direct contact with an infected individual and only occurs through contact with blood and other body fluids,'' Mr Coleman said.
