"For the record, Miss Dudu Myeni is not being investigated by the Hawks," Ntlemeza said in a statement.
"We remain committed to carrying out our mandate of uncovering the truth at SAA and the public will be kept abreast of developments as and when it is necessary."
He said there had been certain media which were "reporting untruths" and he wanted the Directorate For Priority Crime Investigation (Hawks) to distance itself from such reporting.
The Hawks was sanctioned to investigate illegal activities at SAA which include, amongst others, alleged theft, fraud and corruption involving contracts, agreements, tenders, procurement and irregular closure of SAA routes in Senegal, India and Beijing.
The Hawks were also probing allegations of sabotage, irregular use of private investigators to spy and solicit confidential information with a view to undermining SAA operations and the safety of passengers, Ntlemeza said.
Myeni was playing a vital role in assisting the Hawks in this regard, he said.
"...Since we began with the investigations last year she has been very instrumental in providing us with information regarding this important probe."