The country is now trying to trace more than 30,000 people who had either direct or indirect contact with the Liberian virus carrier who collapsed after flying to Lagos on 20 June and died four days later at a private hospital.
"This is a firm confirmation that we had the virus brought to us, and only God knows how far it has transmitted," said Professor Sunday Omilabu, who works on the front line of Nigeria's battle with the virus.
It was in his laboratory at the Lagos University Teaching Hospital that the country's first known case was confirmed.
Professor Omilabu said that they have been trying to reach anyone whose life could be at risk by a potential exposure.
Meanwhile, the federal government has put all ports of entry on red alert and is running a media campaign to alert the public.
Officials said that their health services are equipped to deal with any outbreak and that staff are properly trained.
But residents remain nervous as Lagos, one of Africa's most populous cities, is over-crowded, and its infrastructure and health services struggle at the best of times.
The World Health Organization reported earlier this month that a total of 888 Ebola cases including 539 deaths have been recorded in West Africa since February saying the epidemic has surged in Liberia and Sierra Leone.

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