The Independent Police Investigative Directorate (IPID) will investigate allegations against national police commissioner Riah Phiyega, it said on Tuesday.
"A docket of defeating the ends of justice was referred to the IPID's Western Cape provincial office after it was registered at the Bishop Lavis Police Station," it said in a statement.
"An investigator has been appointed and given an instruction to fast-track the investigation. The investigator will contact all the relevant role players in due course."
The allegations surround claims that Phiyega tipped off Western Cape police commissioner Lieutenant General Arno Lamoer about investigations against him.
Acting IPID director Koekie Mbeki said the decision to probe the matter was in line with the IPID Act.
"As the IPID, we will conduct an independent and impartial investigation and we hope that we will get the necessary co-operation from all parties so that we can expedite this investigation," she said.
"We expect to complete the investigation within three months."
'Committed no crime'
Phiyega welcomed the probe, said her spokesperson Lieutenant General Solomon Makgale.
"The national commissioner still maintain[s] that she committed no crime," he said.
"General Phiyega would like to reassure members of the South African Police Service, as well as the people of South Africa, that she remains focused on her efforts to fight crime and ensure that all police units and officials conduct their tasks with the utmost integrity," he said.
According to reports, Phiyega told Lamoer on three occasions that she was aware he was under investigation.
The Sunday Independent reported that their telephone conversations had been legally recorded by crime intelligence operatives monitoring Lamoer's calls.
He was allegedly associated with a Cape Town drug-dealer and well-known businessperson.
In the conversations, Phiyega reportedly made Lamoer aware of similar allegations by Hawks boss Anwa Dramat.
According to the report, the disclosures outraged crime intelligence operatives, who threatened to lay criminal charges against Phiyega.
Phiyega denied tippingoff Lamoer.
"The national commissioner confirmed that she did not initiate a conversation with Lieutenant General Lamoer with regard to these allegations, but that the conversation arose as a result of a question by a [Democratic Alliance] Member of Parliament," Makgale said.
"The department is obliged to reply to such questions."
He said Phiyega could confirm that she became aware of the inquiry into Lamoer on May 29, after she was briefed by the Hawks.
"An inquiry is an assessment done by the Hawks to establish if there is prima facie evidence to warrant a full investigation prior to opening a docket," Makgale said.
" … Dramat, at the time, indicated that the inquiry was initiated at the request of Lieutenant General Lamoer in July 2012. In other words, Lieutenant General Lamoer has always been aware of the inquiry."
Makgale said the inquiry had at no time been public knowledge.
"Hence Lieutenant General Lamoer's surprise when he found out that a political party was aware of such a matter."
Phiyega previously said it was "interesting" that the allegations against her surfaced from "faceless people" shortly after her decision to put former acting crime intelligence boss Major General Chris Ngcobo on special leave.
Ngcobo was placed on special leave last week after a vetting process allegedly found discrepancies in his qualifications.
Meanwhile, the Democratic Alliance (DA) on Tuesday called for Phiyega's suspension pending the outcome of a probe into the allegations.
"In order to ensure that the investigation is truly independent, Phiyega must be suspended as a course of action to allow the investigation to be conducted without any possibility of her interference," DA MP Dianne Kohler-Barnard said in a statement.
Kohler-Barnard said there were grounds for suspension, under the Labour Relations Act, if an employee was implicated in misconduct, if there was prima facie evidence of guilt, and if the employee could unfairly influence a probe.
"If she is found guilty, we trust that she will be summarily dismissed and formally charged with defeating the ends of justice," she said. – Sapa