Retired public service commissioner John Lloyd told the officer investigating complaints about his conduct she would unlawfully use her power in finding against him.
Mr Lloyd in a letter to merit protection commissioner Linda Waugh attacked the inquiry into allegations raised about an email he sent a right-wing think tank, saying it had been "infected with a denial of procedural fairness".
He claimed he was not told former Commonwealth ombudsman John McMillan, who investigated the allegations against the then-public service commissioner, would probe his decision to send the Institute of Public Affairs a document created by his agency.
Ms Waugh denied the inquiry had been unfair and said Mr Lloyd had never been told it would be limited in the way he claimed, a report tabled in federal parliament found.
Mr Lloyd's letter, sent in response to Ms Waugh's preliminary findings in August, also questioned Professor McMillan's impartiality and referred to a criticism the ex-ombudsman made about him in a media report in 2015.
"I submit that the outcome is that the inquiry has miscarried and its results are invalid," he said.
Under a subheading, 'Moving the Goalposts', Mr Lloyd claimed he was told the investigation would look at whether the document he sent to the institute was created by the public service commission for the think tank, where he is a member and was formerly a director.
Mr Lloyd said then-acting merit protection commissioner Mark Davidson, who preceded Ms Waugh, had told him his decision to email the institute in April 2015 did not justify investigation.
"That decision was a formal final decision, not the expression of a preliminary view. The decision of your predecessor binds you," he told Ms Waugh.
"You are now precluded from making a decision contrary to that made by Mr Davidson."
The inquiry found Mr Lloyd did not use his agency's resources to conduct research for the think tank, but that he had asked the commission's staff to complete it for his purposes as public service commissioner.
It also found he breached a code of conduct governing federal officials by emailing the document created by his agency to the institute.
Mr Lloyd said investigations into his email to the institute were outside the scope of the inquiry, and that any probe into this would be invalid and void. Professor McMillan was not tasked with probing this question, he said.
"To the extent that you have taken into account the views of Professor McMillan, you have not exercised your statutory functions in accordance with the law, as you have taken into account an irrelevant consideration," he told Ms Waugh.
"This muddle could have been avoided if I had been informed of changed terms of the inquiry, had been afforded a reasonable opportunity to be heard, including reasonable access to legal advice and a reasonable time within which to respond to the draft report.
"If I had been so informed, my participation in the inquiry, the evidence I led and the submissions I relied on would have been more extensive and materially different."
Ms Waugh said while it was reasonable for Mr Lloyd to have understood the inquiry was confined to the creation of the document, he was never assured it would be limited to this question, and that he was given two chances from July 25 to respond about his email to the institute.
"While the timeframes for Mr Lloyd to respond have been shorter than I would have preferred, I do consider that they were sufficient for Mr Lloyd to present his case on the particular matter and that he has been provided with procedural fairness in respect of this issue," she said.
The former public service commissioner also said there was a question whether a fair-minded, objective observer would understand that Professor McMillan had shown bias against him, calling into question the inquiry's impartiality and independence in light of the ex-ombudsman's previous media comments.
Ms Waugh said the matter Professor McMillan commented about, freedom of information, was unrelated to the scope of the inquiry.
"I do not believe a reasonably informed bystander would have doubt about Professor McMillan’s ability to bring an impartial mind to his inquiry as a result of this comment," she said.
She said she had brought an independent mind in assessing Professor McMillan's reasoning and reaching her own view about Mr Lloyd's conduct.
Ms Waugh cleared Mr Lloyd of any misconduct on a second complaint her office received about a separate email he sent to institute head John Roskam in October following questioning over his links to the group by Labor senators at a parliamentary hearing.