John Nkengasong, head of the Africa Centres for Disease Control and Prevention, revealed the existence of the new P681H strain.
He believes that it is different to the strains recently discovered in the UK and South Africa.
Medics do not currently think the new strain in Nigeria is more infectious than previous strains, but Dr Nkengasong admitted it was too early to be sure.
"Give us some time ... it's still very early," he said.
The alert about the apparent new variant was based on two or three genetic sequences, he said, but that and South Africa's alert late last week were enough to prompt an emergency meeting of the Africa CDC.
It was found in two patient samples collected on August 3 and on October 9 in Nigeria's Osun state
Earlier, Prime Minister of the UK Boris Johnson stated that a new coronavirus strain was identified in the UK.
The World Health Organization urged Europeans to strengthen approaches to control and prevent the spread of the virus due to the appearance of a new strain of coronavirus in some European countries.
Besides, the new variant of coronavirus is observed in the Netherlands, Denmark and Australia.