Nigeria, Africa's most populous country, on Wednesday confirmed its first cases of the new Covid-19 variant, saying it had been found among three passengers who had travelled to South Africa.
West African neighbour Ghana also said it had recorded the new Omicron variant, tracing cases to Nigeria and South Africa.
Cases of Omicron have been detected in numerous countries since the strain was first reported to the World Health Organization (WHO) in South Africa last week, prompting border closures and travel restrictions.
Nigeria's announcement came as South African President Cyril Ramaphosa visited Abuja during a West African tour where he called for solidarity against "counter-productive" travel bans.
"Genomic surveillance has now identified and confirmed Nigeria's first cases of the B.1.1.529 SARS-CoV-2 lineage, now known as the Omicron variant," said the head of Nigeria's Centre for Disease Control, Ifedayo Adetifa.
Contact tracing and "follow up to ensure isolation... have commenced," Adetifa said.
"Omicron is widespread globally... Therefore, it is a matter of when, not if, we will identify more cases," he said.
Ghana's director-general of health services, Patrick Kuma-Aboagye, said its cases had been detected at Accra's international airport, mainly coming from South Africa and Nigeria.
"The good thing is that in the community test done so far, we have not seen any Omicron within the community of Ghana," he said at the launch of a vaccine campaign.
"But the danger is that if someone has the Omicron, and it is incubating, it will not be found at the airport."
Speaking during a visit with Nigeria's President Muhammadu Buhari in Abuja, Ramaphosa again called on countries to lift "unscientific" flight bans.
"This is a global pandemic and overcoming it requires that we collaborate and work together as a collective," he told reporters with Buhari by his side.
"The resulting damage of this travel ban to the economies of the countries affected will be considerable and long-lasting."
France said Wednesday it would start allowing flights from southern Africa to land on its territory from Saturday, but with "drastic" restrictions allowing only French and EU residents to disembark, along with diplomats and flight crews.
Those travellers will need a Covid test upon arrival, with a negative result still requiring a seven-day quarantine, while a positive test will require a 10-day quarantine, government spokesman Gabriel Attal said.
The coronavirus outbreak has killed 2,976 people and infected 214,113 in Nigeria, according to official statistics, but the real figures are believed to be much higher, in part because of low testing rates.
Home to around 210 million people, the West African nation has launched vaccination campaigns and requires civil servants to show proof of jabs or a negative test to enter public buildings.
But vaccination rates remain low, with just over 6.5 million people given one shot and about 3.5 million people given two shots.
The government said it plans to inoculate around 112 million people, amounting to 70 percent of the adult population, by the end of next year.