The police watchdog alleged that Phahlane was interfering in the investigation against him.
But the police chief gave as good as he got, saying he had not been put into the position by force - and that he could be removed only by the president.
The two parties traded verbal blows in Parliament, where they had been asked to appear by the portfolio committee on police to explain their fight.
This followed a complaint by directorate head Robert McBride two weeks ago that Phahlane was interfering in investigations against him. This was repeated by the Ipid boss on Tuesday, who also called for Phahlane to be suspended pending an investigation.
But Phahlane did not take the accusations against him lying down. He accused the directorate of being used by private investigator Paul O’Sullivan.
He denied he had deployed a unit from the North West to investigate Ipid investigators, who are probing him for corruption. He said it was not his call to be suspended by the president.
“I know Ipid wants me to be suspended. I did not appoint myself as acting national commissioner, I was appointed by the president. I am not glued to the chair of the acting national commissioner,” he said.
He said the investigation against him was being driven by O’Sullivan. “Without any fear of contradiction, Ipid as an independent body doesn’t exist is not functioning.
“Under the current circumstances it might be safe to call it Opid - O’Sullivan’s Police Investigative Directorate,” said Phahlane, suggesting there was a nefarious relationship between O’Sullivan and McBride.
“They (Ipid) have been captured for far too long. We cannot allow Ipid to be utilised to serve people’s personal agendas.”
Phahlane said he had taken the matter to court. He said he had been willing to co-operate with the investigation conducted by Ipid.
McBride denied claims that he had brought in the media during a raid on Phahlane’s house in Pretoria.
This was after Phahlane said he had not been at home when the raid occurred last year. He said there had been several “breaches”, including the questioning of his minor daughter by Ipid.
Major-General Ntebo Mabula denied the police had threatened Ipid officials.
He said they were confining themselves to the threats against Phahlane following an attack at a Joburg spa in June, when robbers broke into the place and stole items from the customers. Phahlane was there with his wife.
Chairman of the portfolio committee on police, Francois Beukman, called on the two units to work together.