Labor has accused Barnaby Joyce of sacking a former agriculture department boss for challenging his integrity.
Paul Grimes last year announced his role as head of the department was terminated citing differences in direction with Joyce, the deputy prime minister and agriculture minister.
At the centre of the dispute were details of ministerial changes to the parliamentary record, which Joyce has blamed a staffer for and which also embroiled the department.
A letter which has been kept secret for more than a year, released on Monday, shows Grimes had no intention of resigning from the job.
He cites a breakdown in the working relationship with the minister.
“I am writing to advise you that I no longer have confidence in my capacity to resolve matters relating to integrity with you,” Grimes wrote to Joyce.
“There are established processes under the Public Service Act for resolving circumstances where a relationship between a secretary and a minister has broken down irretrievably.”
Grimes was stood down just over a week after issuing the letter.
Labor said it was clear that Grimes was first bullied then sacked for trying to protect the reputation of the department.
“A highly respected public servant was sacked because he rightly challenged Barnaby Joyce’s integrity,” the shadow agriculture minister, Joel Fitzgibbon, said.
The government had spent two years and up to $1m in taxpayers’ money trying to “cover up” the affair, Fitziggbon said.
But a spokeswoman for Joyce said the letter was not a direct insight into the working relationships of the department and the deputy prime minister.
Joyce enjoyed a good working relationship with the new secretary, Daryl Quinlivan, the spokeswoman said.
“The deputy prime minister would like to acknowledge Dr Grimes’ long contribution to the Australian public service and wish him well in future endeavours.”
An irretrievable breakdown in relations was also the reason cited by the solicitor general, Justin Gleeson, in his decision on Monday to step down over a row with the attorney general, George Brandis.