Newly-retired public service commissioner John Lloyd breached a code of conduct governing federal officials by emailing a document created by his agency to a right wing think tank, an inquiry has found.

The office investigating allegations of misconduct by the commissioner says Mr Lloyd's actions failed to uphold his agency's good reputation and did not fulfil public service values requiring bureaucrats to "act in a way that models and promotes the highest standard of ethical behaviour."

However in a letter seen by Fairfax Media, merit protection commissioner Linda Waugh on Wednesday said Mr Lloyd's actions were not of "sufficient gravity" to require sanction. Mr Lloyd left his role leading the Australian Public Service Commission the same day.

She found Mr Lloyd was not driven by dishonesty or a lack of integrity, but a failure to recognise the "clear attendant risk" of his actions in emailing the Institute of Public Affairs.

"It was clear that such action would likely be viewed by critics as a strategic and controversial initiative by Mr Lloyd to build a coalition of support for his views, and as a political action, if it were to become publicly known as it subsequently did," Ms Waugh said.

"There were alternative courses (e.g. publishing the document so that its existence and content was available to everyone or passing the request to another senior officer to deal with) available to Mr Lloyd to mitigate these risks, but Mr Lloyd did not choose to do this."

The complaint, received first by the Prime Minister's department in December and later the merit protection commissioner's office, alleged Mr Lloyd breached the Australian Public Service code of conduct by emailing the IPA research about enterprise agreements covering the bureaucracy.

Ms Waugh also 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.

He commissioned the document more than two months prior to a telephone discussion with IPA head John Roskam in April 2015.

"There is no evidence that Mr Lloyd’s action was dishonest, was indicative of a lack of integrity or a misuse of Commonwealth resources," Ms Waugh said.

She also found against an allegation Mr Lloyd had a conflict of interest in sending the document given his duties as an agency head "with a wide discretion to conduct the affairs of his agency and to advance public debate on agency matters".

"While I have found that there were actions Mr Lloyd could have taken that would have minimised any such perception, I consider that those actions bear more greatly on his obligation to uphold the APS Values ... and the good reputation of the APSC and the APS," Ms Waugh said.

Mr Lloyd declined to comment. His term as commissioner was due to expire in December 2019, but he abruptly announced in June he would resign from his $706,000 a year job while denying the timing was influenced by a possible investigation.

The Australian Public Service Commission said then he had "for some time" considered departing before his term as commissioner ended, and Mr Lloyd later told senators he had felt it was time to resign after a long career.

In a valedictory speech on Monday to public servants in Canberra, Mr Lloyd said he found the process by which he remained under an unfinished investigation "most unsatisfactory".

Former federal ombudsman John McMillan conducted an independent investigation into the allegations Mr Lloyd breached the public service code of conduct, after the former acting merit protection commissioner Mark Davidson engaged him for the probe.