"Insiders have told us that when he left his office in Pretoria late yesterday, he said goodbye to most of his staff members saying he will not be returning to the office on Monday."
On Friday, prosecutors announced they would charge Selebi with corruption, fraud, money laundering an racketeering.
Selebi, an ally of Mbeki, has denied any wrongdoing.
His legal team went to court on Friday to try to prevent his prosecution, but the judge rejected the application.
Selebi's indictment covers a range of offences, including receiving payments from his friend, Glenn Agliotti, a convicted drug smuggler accused of playing a role in the murder of a South African mining magnate, Brett Kebble in 2005.
The decision to charge Selebi is likely to raise fears of political instability in South Africa, where Mbeki and his rival, Jacob Zuma, the new leader of the ruling African National Congress (ANC), are locked in a power struggle.
Zuma was charged with corruption, fraud, money laundering and racketeering less than two weeks after he won the party leadership from Mbeki last month.
This fuelled allegations that the charges had been used as a political weapon.
Court papers filed by the national prosecuting authority (NPA) before the decision to charge Selebi said he faced no prospect of imminent arrest and that arrangements over a court date would be reached with the police chief's lawyer.
Mokotedi Mpshe, the NPA's acting director, said "I don't think it is going to be that long" before Selebi is charged.
Gerrie Nel, a senior official of the Scorpions, an elite unit of the NPA, who was leading the investigation into Selebi, has also been arrested on corruption charges.