The investigation into Mr Lloyd's decision to email a document to pro-free market think tank the Institute of Public Affairs - where he was a member and former director - ended with a finding in August he failed to uphold his agency's good reputation.

Mr Lloyd, who retired that month, has told a Senate committee the inquiry findings had damaged his reputation and rejected its finding he had failed to meet high ethical standards.

"The impact of the adverse references was amplified by what I consider were most unsatisfactory processes adopted in the handling of the complaints leading to the report," he said.

"My rights to a fair hearing were not respected."

Mr Lloyd, whose tenure leading Australia's public service commission was marked by a protracted round of enterprise bargaining and clashes with the main public sector union, claimed his role had been to challenge union tactics.

He rubbished the code of conduct inquiry finding that his decision to send the IPA a document outlining what he described as "generous" conditions in the bureaucracy's workplace agreements would be seen as building "a coalition of support for his views".

"The opponents employed a range of tactics with vigour to build support for their position. It would be contrary to my obligation as APS commissioner, responsible for the good reputation of the APS, not to build support for the policy position of the government," Mr Lloyd said.

In his statement to the Senate committee in charge of protecting people referred to under parliamentary privilege, he also rejected the inquiry's finding he could have directed the IPA to access the document through a freedom of information request, or directed his media office to respond instead.

Mr Lloyd attacked the inquiry's conduct, alleging he was not told of a potential conflict of interest for the ex-ombudsman tasked with investigating the complaint about the email to the think tank.

Ex-federal ombudsman and former information commissioner John McMillan had made comments to The Guardian in 2015 criticising his views on freedom of information, Mr Lloyd said.

Professor McMillan denied there was a conflict on Thursday, saying he had declared the media interview when asked to investigate the complaint against Mr Lloyd. The comments were not a personal criticism of the former public service commissioner, he said.

He found the comments did not prevent him from conducting the inquiry and the official who asked him, then-acting merit protection commissioner Mark Davidson, had agreed.

"My view was that any criticism by a senior official that FOI 'has gone too far', should explain what it is meant by 'too far'. My comments were about the administration of FOI, which was an issue for which I had responsibility for over four years as an independent statutory officer," Professor McMillan said.

"There was no logical basis for supposing that in light of my reported views on FOI administration three years previously I would not bring an open mind to the allegations I was asked to investigate relating to Mr Lloyd.

"I had no prior familiarity with those issues or the IPA, and I had not expressed any view upon them."

Professor McMillan said it was never suggested previously that the criticisms about federal or state administration he had made in previous reports disqualified him from conducting inquiries on other matters.

Mr Lloyd also said he wasn't told the scope of inquiry had expanded beyond questions of the purpose for the document's creation.

New merit protection commissioner Linda Waugh, who made the finding against Mr Lloyd after receiving Professor McMillan's report, has previously rejected the former public service commissioner's complaints about the inquiry.