Justice ministry spokesperson Paul Setsetse said Minister Penuell Maduna had opposed a pardon because Boesak had "failed to acknowledge in his application that he had committed an offence".
Mbeki had yet to make a decision on the matter.
He would inform Boesak of his decision in due course, Setsetse said.
Boesak was jailed in 2000 for the theft of donor funds from his Foundation for Peace and Justice. He completed his three-year sentence earlier this year.
On Wednesday, he boycotted a function to celebrate the 20th anniversary of the founding of the United Democratic Front, claiming the ruling African National Congress had "ostracised, ignored and discarded" him. – Sapa.
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