The National Emergency Management Agency (NEMA) said the building -- thought to be a guesthouse for foreign members of TB Joshua's The Synagogue Church of All Nations (SCOAN) -- came down in the city's Ikotun area.
"We have three dead. Scores of others are still trapped. Eighteen were rescued alive and have been taken to various hospitals," NEMA's southwest coordinator Ibrahim Farinloye told AFP from the scene.
TB Joshua, dubbed "The Prophet", has an almost fanatical following among many Nigerians and others across the world, who are attracted by his purported healing powers and prophecies.
"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.
Farinloye said NEMA rescuers were joined by their counterparts from the Lagos State government, local police, civil defence forces and building control officials.
Construction work had apparently started to add extra storeys onto the two-storey building inside the church compound when the collapse happened, he added.
Farinloye and an AFP photographer at the scene said security officials attached to the church tried to prevent rescue workers and the media from accessing the site.
"They were attacking responders," Farinloye said, while the photographer said television crews had their cameras broken.
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