Phahlane was moved back to his position as head of forensic services, and regional commissioner for the police Lt-Gen. Lesetja Mothiba has been appointed the new acting national commissioner.
But Phahlane was requested by Police Minister Fikile Mbalula to immediately give reasons why he should not should not be suspended from his old position.
Mbalula noted that the department has acted quickly against Phahlane, following the allegations against him.
But Mbalula said due process had to be followed before action could be taken.
Mbalula also said the police would have a permanent head by August as suspended commissioner Riah Phiyega’s contract ends on 10 June.
Mbalula said there were serious allegations of misconduct against Phahlane which impacted on his fitness to hold office.
“The allegations against Phahlane raises questions of conduct that is inconsistent with expectations that South Africans have of those who hold leadership positions in our police service,” he said.
He added the allegations against Phahlane were serious and posed a threat to the Independent Police Investigative Directorate (Ipid).
Ipid accused Phahlane of setting up a special unit from North-West to harass its investigators.
But Phahlane hit back, accusing Ipid of flouting the law in their investigation and using private investigator Paul O’Sullivan.
He said the unit was looking into his safety after he was attacked during a robbery in Joburg in June last year.