The Australian Greens say the most senior federal government watchdog has been "politically assassinated".
Commonwealth Ombudsman Allan Asher announced his resignation on Thursday, only 14 months into a five-year term.
Mr Asher faced pressure from the government after admitting he had scripted questions for Australian Greens senator Sarah Hanson-Young about his inadequate funding and increasing workload, to be asked at a parliamentary estimates hearing in May.
"It is with sadness that I made the decision to tender my resignation," Mr Asher said in a statement.
"But I have done so because I recognise that the office of the commonwealth ombudsman's enduring strength lies in community confidence in its integrity."
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Mr Asher said he accepted that his actions had called into question the impartiality of his office.
But he said he hoped the episode would spark public discussion about the future funding of his office and ways it could be made more accountable.
Greens leader Bob Brown said Mr Asher was a "decent man working in the public interest".
"(He's) been politically assassinated," Senator Brown said.
"His crime was to supply non-political questions - rather than answers - to Greens Senator Sarah Hanson-Young, as a means of getting information on the public record."
Deputy ombudsman Alison Larkins will act in the position.
Senator Brown said there was a clear message for future applicants for the job.
"Forget the public interest, keep your head down, make no waves and listen carefully for the dog whistle of political obedience," he said.
Special Minister of State Gary Gray said the ombudsman's role was an important institution.
"It is a critical part of our system of government accountability and it needs to maintain the highest standards of independence, impartiality and integrity in carrying out this responsibility," he said.
He thanked Mr Asher and his staff for their "professionalism, commitment and dedication".
Opposition Leader Tony Abbott earlier told reporters he understood there had been questions raised about Mr Asher's conduct.
"I just make the fundamental point that it says something about the dysfunction at the heart of this government that a senior statutory officer feels it necessary to get questions asked of himself in estimates, rather than simply being able to approach the government in the normal way," Mr Abbott said.
When parliament resumes in November, the Greens plan to seek approval for the ombudsman to regularly report to the public accounts and audit committee.
