Public service commissioner John Lloyd has said he is not under investigation after the Prime Minister's Department admitted it received an allegation he breached the law.
Department of Prime Minister and Cabinet officials told a Senate estimates hearing on Tuesday its secretary Martin Parkinson referred the matter to the Merit Protection Commissioner a month after receiving the allegation in December.
After Mr Lloyd refused at an estimates hearing on Monday to say whether or not he was the subject of a probe despite repeated questioning, a letter he wrote presented to the Senate committee late on Tuesday said he was not under investigation.
PM&C; deputy secretary Stephanie Foster earlier would not outline the allegation, and the acting Merit Protection Commissioner, Mark Davidson, refused to comment when Fairfax Media asked whether he or his office had started an inquiry.
Questions about a possible probe were raised last week after it emerged the Prime Minister's Department in April refused to release two emails relating to Mr Lloyd and a right-wing think tank when responding to a freedom of information request, saying it could prejudice an investigation.
Officials have said the FOI decision referred to a possible investigation only, and that the department's involvement with the matter ended when Dr Parkinson referred it to the Merit Protection Commissioner.
Mr Lloyd has previously denied giving special access and research to the Institute of Public Affairs after Labor last year raised an email he sent to a member of the group with an attachment showing what he described as "generous" provisions in public service enterprise agreements.
When asked whether he was under investigation on Monday, Mr Lloyd refused to answer and initially said his role required him not to disclose the identity of people subject to an investigation.
He later said he would take on notice the basis on which he could make a public interest immunity claim not to answer questions about an investigation, but did not give a deadline before which he would respond to that question.
In confirming he was not under investigation on Tuesday, Mr Lloyd said he would no longer make a claim to public interest immunity after receiving advice.
Ms Foster told Labor senator Penny Wong at Senate estimates that Mr Davidson was able to conduct an inquiry into alleged breaches of the Australian Public Service code of conduct by the public service commissioner, and was required to report on its results.
The Merit Protection Commissioner, who holds an independent role, conducts inquiries into whether public servants have breached the code and shares an office and staff with the Australian Public Service Commission.
A freedom of information request in January sought emails held by Dr Parkinson mentioning Mr Lloyd and the IPA, and dated from October 23, after senators referred to an email in a Senate estimates hearing.
The department responded to the request last month by refusing to release two emails in Dr Parkinson's inbox, dated December 20 and December 22.
"I am satisfied that disclosure of the documents could reasonably be expected to prejudice the conduct of an investigation of a breach, or possible breach, of the law in a particular instance," assistant secretary Peter Rush wrote.
Releasing the documents could also "reasonably be expected to prejudice the impartial adjudication of a particular case", Mr Rush said.
Mr Lloyd is a member of the IPA. Before the Abbott government appointed him APS commissioner in 2014, he was the director of the think tank's work reform and productivity unit.