Australian Public Service Commissioner John Lloyd on Monday refused to say if he was under investigation but on Tuesday a Senate committee heard there had been allegations made against him in his role as commissioner.
Stephanie Foster, who heads up the governance section of the prime minister's department, confirmed an allegation had been made against Mr Lloyd in his role.
She said the allegation was received on December 13 and on January 11 it was sent to the Merit Protection Commissioner.
Mr Lloyd refused on Monday to answer any questions about it but finally revealed on Tuesday he is not being investigated.
"I confirm that there is no inquiry being conducted to which I am the subject," Mr Lloyd said in a letter to the committee on Tuesday.
Mr Lloyd argued that people who were subject to inquiries should have their privacy respected.
The allegation came to light when a freedom of information request for Mr Lloyd's emails was rejected on the grounds it could prejudice an investigation.
Australian Associated Press