A Liberian man who died in Nigeria's megacity of Lagos on Friday has tested positive for the deadly Ebola virus, the country's health minister has confirmed.

The man, who was in his 40s, collapsed on arrival in Lagos, a city of 21 million people, on Sunday, and was taken from the airport and put in isolation in a local hospital.

Nigerian Health Minister Onyebuchi Chukwu said all ports of entry in the country are now on "red alert" and health officials are investigating all people who had contact with the deceased.​

Earlier on Friday, a Nigerian official in Geneva said the man died while under quarantine.

"The Liberian came in and he was quarantined at the airport and not allowed to go to the city. While he was quarantined he passed away. Everyone who has had contact with him has been quarantined," he told Reuters.

Ebola, one of the world's deadliest diseases, has killed 660 people across Guinea, Liberia and Sierra Leone since it was first diagnosed in February. There have been 1,093 cases to date in West Africa's first outbreak, according to the UN health agency.

The Liberian man is the first case on record of Ebola in Nigeria, Africa's biggest economy and, with 170 million people, its most populous country. 

"He departed on the plane initially with no symptoms, he reported being symptomatic on arrival. I understand that he was vomiting and he then turned himself over basically, he made it known that he wasn't feeling well. Nigerian health authorities took him and put him in isolation," World Health Organization spokesman Paul Garwood said earlier on Friday