"... The provincial commissioner is unable to respond to the media at this stage," said Colonel Tembinkosi Kinana.
Lamoer would address the media at an "appropriate time", he said.
The Sunday Independent reported that Phiyega told Lamoer on three occasions that she was aware he was under investigation.
Drug dealer connections
According to the newspaper, these telephone conversations were legally recorded by crime intelligence operatives monitoring Lamoer's calls after allegedly showing that he was associated with a Cape Town drug-dealer and well-known businessman.
In the conversations Phiyega reportedly made Lamoer aware of similar allegations by Hawks' boss Anwa Dramat.
The newspaper reported that its sister newspaper, The Sunday Tribune, had heard the taped conversations.
According to the report, the disclosures had outraged crime intelligence operatives, who had threatened to lay criminal charges against Phiyega.
The Independent Police Investigative Directorate confirmed on Friday that it had received allegations of defeating the ends of justice against Phiyega.
The case was reported on Wednesday.
Crime intel boss on special leave
The Star reported on Friday that Phiyega allegedly tipped off a senior police officer, who allegedly accepted a bribe from a criminal, that he was being investigated by crime intelligence.
However, Phiyega denied doing so, and said he had become aware of the investigation after the opposition Democratic Alliance asked a question about it in Parliament.
Also, Phiyega said it was "interesting" that the allegations against her had 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 this week after a vetting process allegedly found discrepancies in his qualifications.
Phiyega said she had not been formally informed of the case of defeating the ends of justice against her, but was aware of the allegations.