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FUL also applied for an interdict against Police Minister Nathi Mthethwa, preventing him from moving Mdluli to a new position before a review into his reinstatement could be heard.
The case will be heard by the Pretoria High Court on June 5.
Anti-apartheid activist and FUL member Mamphela Ramphele said in the organisation's founding affidavit that former police commissioners Jackie Selebi and Bheki Cele were suspended by Mthethwa for "less serious criminal charges" than Mdluli's.
"The way ... Mdluli had been dealt with by the respondents reflects an extraordinary degree of a lack of accountability and a breach of a culture of justification," said Ramphele.
She said Mdluli's letter, which plotted out a conspiracy against him, had generated mistrust and instability in the South African Police Service.
The letter, written by Mdluli in November, was addressed to President Jacob Zuma, Mthethwa and acting national police commissioner Nhlanhla Mkhwanazi.
In it, Mdluli reportedly wrote that Cele, Hawks head Lieutenant-General Anwa Dramat, operational services head Lieutenant-General Godfrey Lebeya and Gauteng police commissioner Lieutenant-General Mzwandile Petros were ganging up against him.
Ramphele said the task team, appointed by Mthethwa to investigate the allegations in the letter, would not resolve "the problem" caused by Mdluli's reinstatement.
"By his conduct, the minister accepted that there was a need to act, but has not initiated suspension proceedings, or any other measure which would remove ... Mdluli from active daily service in SAPS," she said.
On May 9, Mthethwa announced that Mdluli would be shifted from his position to another division.
Last year, Mdluli faced fraud and corruption charges relating to alleged misuse of a crime intelligence fund, the purchase of luxury vehicles and the hiring of family members.
He also faced a murder charge for the alleged murder of the boyfriend of his former girlfriend.
Both sets of charges were withdrawn and Mdluli was reinstated as head of crime intelligence.
The murder investigation became an inquest. - Sapa