Authorities in Lagos had previously said that the death toll was 61 and there has not been any explanation for the discrepancy in numbers.
A guest house was being built at The Synagogue, Church of All Nations – led by 'prophet' TB Joshua – when it collapsed on Friday, leaving hundreds trapped.
According to reports, 131 people were taken to hospital for treatment.
President Jacob Zuma said: "This is a particularly difficult time for South Africa. Not in the recent history of our country have we had this large number of our people die in one incident outside the country.
"The whole nation shares the pain of the mothers, fathers, daughters and sons who have lost their loved ones."
In a statement, the South African government said that "at least five South African church tour groups were at the Synagogue at the time of the collapse".
Thousands of people from across Africa travel to TB Joshua's church amid claims that he has healing powers and can cure illnesses such as HIV and AIDS.