Deputy Prime Minister Barnaby Joyce has denied altering the official record of Parliament and sacking the Agriculture Departmental secretary over a breakdown in their working relationship.

The Nationals leader has faced criticism from Labor this week after the release of a letter from former secretary Paul Grimes that raised questions about Mr Joyce's conduct and "integrity".

The federal government spent 18 months and tens of thousands of dollars trying to keep secret the letter from Dr Grimes, written 10 days before he was sacked amid controversy about changes to Hansard in which some of Mr Joyce's statements to Parliament were quietly altered.

Maintaining he never altered Hansard, Mr Joyce told ABC radio on Thursday he had not sacked Dr Grimes.