"We understand from our assessment team that the total number of people who have perished is now 115, but those are not all South Africans," said Jeff Radebe, the minister in charge of Pretoria's response to the disaster.
The casualties include 84 South Africans, said Radebe, speaking after around two dozen injured survivors were repatriated home.
Ten days after the disaster, Nigerian officials struggled to immediately confirm the death toll.
"There could have been additional deaths on arrival at the hospitals," suggested rescuers' spokeperson Ibrahim Farinloye, of the National Emergency Management Agency (NEMA).
He said it was now up to the church and the various embassies to give the exact final toll.
Minister Radebe revised the numbers of injured that arrived to 25, because one refused to board the medical evacuation plane in Lagos and chosen to return to the church which crumbled in Lagos on September 12.
The plan was to bring back all the 26, but "there were only 25 who actually boarded the aircraft because one returned to the synagogue yesterday," said Radebe.
The 26 survived after being trapped under rubble when a guesthouse attached to the church run by a prominent Nigerian preacher TB Joshua collapsed more than a week ago.
A 19-member medical team including specialised doctors, nurses and medical military paramedics took care of the injured on board a military C-130 aircraft.
"It's the biggest evacuation effort by the (South African) Air Force since the dawn of democracy," two decades ago, said Radebe.
Two orphaned toddlers - that lost their parents in the tragedy - were among the survivors that returned on Monday.
Sixteen of the wounded were in critical condition, with some having had limbs amputated and one developed gangrene in the toes.
Others had developed kidney failure and were on dialysis.
They were loaded from the aircraft at Swartkop Air Force Base onto ambulances and driven to Steve Biko Academic Hospital in the capital Pretoria.
Some 350 South Africans were thought to be visiting the church in the Ikotun neighbourhood of the megacity of Lagos when the three-storey building came down during construction work.
Joshua, one of Nigeria's best-known evangelical preachers, on Sunday pledged to visit South Africa to meet survivors and their families.
Radebe thanked the "Nigerian government for the cooperation that they have had with us in order to ensure we executed this task as a matter of extreme urgency."
"We are keenly awaiting, as the South African government, for the investigation that is being conducted by the Nigerian government so that we get to the bottom of the cause of the collapse of this building that has caused us this national disaster," he said.
Farinloye said the first investigation meeting would be held Tuesday involving state and federal bodies as well as engineers to assess the collapse, its causes and determine next steps.
Nigerian President Goodluck Jonathan visited the church on Saturday and promised to investigate the cause of the tragedy.
But South Africa's largest opposition party the Democratic Alliance would like the government to sue the church over the deaths.
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