A former head of the Agriculture Department was deeply concerned about Agriculture Minister Barnaby Joyce's handling of changes to the official parliamentary record, a long-secret letter has revealed.

Key points: Barnaby Joyce had to correct Hansard record in 2014, but blamed rogue staffer when original record was altered

Barnaby Joyce had to correct Hansard record in 2014, but blamed rogue staffer when original record was altered "Hansardgate" sparked events that led to toxic relationship between Joyce and Ag head

"Hansardgate" sparked events that led to toxic relationship between Joyce and Ag head Ag head Paul Grimes left position in 2015

In the March 2015 letter, Paul Grimes told the now-Deputy Prime Minister he "no longer [had] confidence in [his] capacity to resolve matters relating to integrity" with him.

The bad blood stemmed from an incident in October 2014, when Mr Joyce told parliament that farmers in financial need had "immediate" access to the Farm Household Allowance.

In fact, farmers in drought were waiting weeks and months for access to the income support payment.

Mr Joyce later re-entered the chamber to correct the record, but the Hansard record of his original answer was also subsequently changed. Mr Joyce blamed a rogue staffer.

But the so-called "Hansardgate" incident sparked a chain of events that deepened the toxic relationship between Mr Joyce and Mr Grimes, and culminated in the effective dismissal of Mr Grimes as secretary.

Labor has pushed for the Government to release Mr Grimes' letter for more than a year, but the department had resisted freedom of information requests for correspondence between the minister and his public service officials.

The department said that "due to the passage of time", it had withdrawn its appeal to keep the letter secret.

Opposition agriculture spokesman Joel Fitzgibbon used the Senate Estimates process to pursue the matter, including in an extraordinary additional hearing last year.

Mr Fitzgibbon said the letter revealed Mr Grimes "was first bullied and then sacked for standing up to Barnaby Joyce over his Hansard cover-up".

"Barnaby Joyce told the House of Representatives a member of his staff made the changes without his knowledge. Pigs might fly too," Mr Fitzgibbon said in a statement.

A spokeswoman for Mr Joyce said the letter "is not a direct insight into the working relationships of the department and the Deputy Prime Minister, and has not been for more than 17 months".

The spokeswoman said Mr Joyce enjoyed a "good working relationship" with his current secretary, Daryl Quinlivan.

Farmers still facing long wait for income support

Meanwhile, farmers continue to face long delays for access to the Farm Household Allowance that Mr Joyce said was "immediately" available to farmers in 2014.

The ABC has revealed that South Australian dairy farmers hoping for urgent financial relief have waited up to six months for money to come through from the Federal Government.

The organisation charged with administering the payments in South Australia agreed the problem was widespread, saying the complexity of the application process was a major issue.

Anecdotal reports from other states indicated their support services had also been stretched by rising demand.

The pressure was no longer just coming from drought-affected farmers, but from dairy farmers affected by the milk price crash, and from farmers who had faced major flooding in recent months.