One of the soldiers manning the main entrance to the Swartkop Air Force Base in Pretoria said the plane would touch down after 10:00.
“The cause of the delay, I do not know but it (the plane) will not be arriving now,” said the soldier who did not want to give his name.
An advisory issued by the Government Communication and Information System on Sunday said the plane was set to land at the Swartkop Air Force Base in Pretoria at 07:00.
An inter-ministerial task team led by Presidency Minister Jeff Radebe is set to welcome the patients from Lagos.
Eighty-six people were killed when a guesthouse belonging to the church collapsed on September 12.
Amongst those killed were 84 South Africans.