The Public Health Agency (PHA) confirmed to the BBC that the person has been placed in isolation since Friday.
It said the person recently travelled in an Ebola affected area and was being assessed and tested in accordance with a national contingency plan.
Having already tested positive for malaria, a blood sample will confirm if they also have contracted Ebola.
The BBC understands the patient has been in the Royal Victoria Hospital's special isolation unit since Friday.
In line with national guidelines, nursing staff are wearing protective clothing while caring for the patient.
Last month, it was announced that senior doctors in Northern Ireland had been putting contingency plans in place for an outbreak of Ebola.
Within the last fortnight, health care staff across all the local health trusts took part in a mock exercise in preparation for such an event.
The PHA said it is keeping in regular contact with staff across the health service and has advised that there is no increased risk to other patients or the wider community.
Low risk
Ebola virus disease (EVD), formerly known as Ebola haemorrhagic fever, can be a severe illness in humans.
The incubation period, that is, the time interval from infection with the virus to onset of symptoms, is two to 21 days.
It is important to note that the likelihood of contracting EVD is extremely low, unless the person had come into contact with blood or body fluids of a symptomatic person.
The PHA stressed that the risk to the public is low.
It said there was no change to the current situation in Northern Ireland in that the risk to the public was very low.
By Marie-Louise Connolly: BBC News NI Health Correspondent
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