Monwabisi Mbeki's mother Nokwanda Mpahlwa, a Transkei nurse, was among those who testified before the Truth and Reconciliation Commission in Port Elizabeth last week.
Mpahlwa said Mbeki's family had told her that 21-year-old Monwabisi - the result of a high-school romance - went missing between Vereeniging and Durban in 1981 while looking for another Mbeki relative, Phindile Mfeti.
She said Mbeki had gone into exile in London and had only seen the boy once when he was two. Monwabisi had "worshipped" his father and had complained about not seeing him.
A spokesman for Mbeki's office Ricky Naidoo told Sapa on Monday that the Deputy-President had exhausted all avenues in his efforts to trace his son.
"However, he will continue to pursue his inquiries at all levels to come to some sort of resolution.
"He will keep pursuing the matter with the police, although he does presume his son is dead given the fact that there has been no word on his whereabouts."