"The president came to the church this morning to see things for himself. He met with Prophet T B Joshua and expressed his condolences to the bereaved families," Ibrahim Farinloye of the National Emergency Management Agency told AFP.
He said Jonathan promised to investigate the cause of the September 12 collapse of the guesthouse at Synagogue Church of All Nations (SCOAN) which left scores trapped in the debris.
Farinloye said the death toll now stood at 86 as against the previous figure of 84 after the various emergency teams involved in the operation had reconciled their figures.
Farinloye could not say if the new death toll included 84 South Africans who had been confirmed dead in the incident by the country's high commissioner to Nigeria Lulu Mnguni.
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It is believed that there were 349 South Africans visiting the popular church in the Ikotun district of the city at the time of the collapse.
The church's leader Joshua, who has blamed the incident on sabotage, is one of Nigeria's most well-known Pentecostal preachers and is referred to by followers across the world as "The Prophet" or "The Man of God".
The Lagos state government has accused the church of adding extra floors to the existing structure without approval.
It has ordered urgent structural integrity tests on all buildings in the sprawling compound, including the main church, which Joshua says was designed by the Holy Spirit.