Ibrahim Farinloye, southwest coordinator for the National Emergency Management Agency (NEMA) told AFP yesterday in a text message that the death toll was 17.
Another 124 people were rescued alive from the rubble of the building in the Ikotun area of Lagos.
The agency said earlier that at least three people were known to have died when the building -- thought to be a guesthouse for foreign members of TB Joshua's The Synagogue Church of All Nations (SCOAN) -- came down on Friday.
Rescue operations were ongoing, Farinloye said.
TB Joshua, dubbed "The Prophet", has an almost fanatical following among Nigerians and across the world, attracted by his purported healing powers and prophecies.
Joshua preaches to massive crowds at his megachurch in Ikotun every week and, according to his website, SCOAN "hosts thousands of national and international visitors" each year.
"People travel from around the world to witness and receive from the mighty work that God is doing in the life of Prophet TB Joshua," it states.
Joshua said on his Facebook page TB Joshua Ministries that reports that the church auditorium had collapsed and that there had been heavy casualties were not correct.
"The few people that were there are being rescued," he said.
The website of Nigeria's The Guardian newspaper quoted Joshua as saying that a low-flying plane that had been repeatedly circling the building may have been responsible for the collapse.
Ikotun lies to the west of Lagos' international airport.
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