"He had earlier engagements. There's been a confirmation from his family that four members of his family will attend and one of them will be speaking," said ANC spokesperson Keith Khoza.
There was a misunderstanding about whether Mbeki would make it to the lecture in Aliwal North, but this had been cleared, said Khoza.
The lecture forms part of a series of ANC centenary lectures on the lives of its past presidents.
Mbeki's spokesperson Mukoni Ratshitanga confirmed that he would not attend.
"The former president is not going to attend the lecture due to prior commitments that have to do with his responsibilities around the two Sudans," Ratshitanga said.
"He won't be out of the country, but [will be] engaged with this process."
Mbeki recently criticised the ANC leadership for losing its ability to provide direction to South Africa.
"I … [am] deeply troubled by a feeling of great unease that our beloved motherland is losing its sense of direction, and that we are allowing ourselves to progress towards a costly disaster," he said in his Oliver Tambo memorial lecture at the University of Fort Hare, in the Eastern Cape.
Afterwards, ANC chairperson Baleka Mbete said Mbeki was entitled to speak out against the ruling party.
"He's contributing to the debate, he's expressing a view," she said. – Sapa