Speaking while on an election campaign trail in Mafikeng, Mbeki said the that country had asked South Africa for help in ensuring that the trial of the arrested men be transparent and fair.
"It was a direct request," Mbeki said.
He said South Africa would not be doing the same in Zimbabwe simply because the Zimbabwean government had not made the same direct request.
He said Foreign Affairs Minister Nkosazana Dlamini-Zuma was currently working with an Equatorial Guinea delegation on the issue.
South Africa has also agreed to help the west African country with its investigation into the alleged plotted coup.
He said officials from South Africa, Zimbabwe and Equatorial Guinea were working closely together on the issue.
On the threat that the arrested men in Zimbabwe would face the death penalty, Mbeki said no charges had been laid against the men and it was doubtful people would be sentenced to death for fraud.
"But no charges had been preferred, and I can't speculate on possible sentences," he said.
Mbeki said some of the men arrested in Zimbabwe and Equatorial Guinea were known to the South African security organisations and some were former SA Defence Force members.
He said South Africa would definitely charge anyone of the men who was suspected of contravening the Foreign Military Assistance Act. Sapa.
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