The Department of Agriculture boss has contradicted his minister's claims he willingly resigned over a breakdown of relations.
Agriculture Minister Barnaby Joyce on Friday announced Paul Grimes would step down after agreeing with a report from the prime minister's office that the pair no longer shared a "mutual confidence".
But in a notice to his staff, Dr Grimes said his appointment had been terminated.
The secretary said he was disappointed to be leaving the department but fully accepted the decision.
"I have agreed that the minister would be better supported at this time by a new secretary with a different background and set of policy skills," Dr Grimes said in the email.
Dr Grimes has been on leave since last Friday after seeking a specially-convened Senate estimates hearing to address concerns about a Labor freedom of information request relating to a Hansard correction by Mr Joyce's office last year.
The opposition accused Mr Joyce of misleading parliament over the correction to the official record of parliamentary proceedings.
The minister later blamed staff for the correction, and Speaker Bronwyn Bishop found there were no grounds for misconduct action against him.
Dr Grimes had written to the Senate committee to give "highly pertinent" information at the extraordinary hearing about the FOI request sought by Labor's agriculture spokesman Joel Fitzgibbon.
But he did not reveal such detail and took most questions on notice.
Mr Fitzgibbon said Dr Grimes' departure was no accident.
"He stood up to the minister," Mr Fitzgibbon tweeted.
In a statement, Mr Fitzgibbon said Prime Minister Tony Abbott should sack "his incompetent minister" Mr Joyce.
He called on Mr Abbott to detail his reasons for requesting the termination of Dr Grimes' tenure.
"On what basis did the prime minister recommended to the Governor-General the distinguished career of Dr Grimes be terminated?" he asked.
Mr Fitzgibbon claimed the sacking was the result of Dr Grimes telling the truth about what he labels "hansardgate".
He accused Mr Abbott of "covering" for the agriculture minister.
"The saga has dragged on long enough and has now cost a distinguished public servant his job," he said.
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