The Nigerian Centre for Disease Control (NCDC) says it has detected the Omicron variant in travellers from South Africa who arrived in Nigeria last week.
In a press release, the body warns that it is a matter of "when, not if" more cases are identified.
The organisation says its research suggests that given the likely high transmissibility of the variant, it is imperative to introduce measures to curb community transmission like "increased COVID-19 testing".
Earlier this week, the government of Canada said that it had discovered two cases of the variant from two passengers from Nigeria.
However, the Nigerian health authorities said that it was investigating the issue to get more details.
Canada has now added Nigeria to the list of countries where travellers are barred from entering into its territory, following the discovery.
Omicron has been rated by the World Health Organization as a "variant of concern".