They have been accused of using their power to settle political scores, most notably in the case of Jacob Zuma, the African National Congress leader (ANC), who has been charged with corruption.
The Scorpions, who were established by Mbeki in 1999 to fight high-profile corruption cases, are not part of the police and report to the National Prosecuting Authority (NPA).
The NPA answers to South Africa's justice department.
In 2005 the Scorpions raided properties belonging to Zuma and his lawyer as part of a corruption inquiry against him.
The action prompted the pro-Zuma wing of the ruling party to brand the unit a political tool of Mbeki and push for it to be incorporated into the police.
The ANC passed a resolution to do so in December after overwhelmingly electing Zuma as leader in a two-man contest with Mbeki.
Mbeki had tried to fight to keep the Scorpions intact.
In 2004 the Scorpions arrested Mark Thatcher, the son of Margaret Thatcher, the former British prime minister, in connection with a plot to overthrow the government of Equatorial Guinea.