Jackie Selebi, the head of the international police organisation, Interpol, and South Africa's national police chief, is set to be charged with two counts of corruption.
The National Prosecuting Authority (NPA) said on Friday that attempts by his legal team to prevent his prosecution had failed.
"A decision has been made, he will be charged with corruption and defeating the ends of justice," Tlali Tlali, a spokesman for the NPA in Cape Town, said.
Selebi, an ally of Thabo Mbeki, the South African president, has denied any wrongdoing.
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.
The NPA charged Zuma 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 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.
The charges against Nel, who is due in court on Monday, include fraud and "defeating the ends of justice".
Selebi is accused of receiving money from Agliotti on several occasions, including $4,400 for a dinner in Paris to celebrate his appointment as president of Interpol.
The indictment says that between 2000 and 2005 Selebi received at least $177,000 from Agliotti and his associates.
Selebi's friendship with Agliotti has put him under the spotlight as South Africa has one of the world’s worst rates of violent crime.
His police force is under mounting pressure to make the streets safe before South Africa hosts the football World Cup in 2010.