The head of the federal Department of Agriculture, Paul Grimes, has gone on unscheduled leave amid growing speculation of a fractured relationship with Agriculture Minister Barnaby Joyce.

Fairfax Media has learnt that Dr Grimes did not turn up to work a day after fronting a specially convened additional Senate estimates hearing at Parliament House last Thursday.

Dr Paul Grimes. Credit:Edwina Pickles

Unusually for a department head, Dr Grimes had requested the hearing, which allowed Labor senators a further chance to explore issues around his department's knowledge of an incident last year when Mr Joyce's ministerial staff altered the official transcript of Parliament to correct remarks made by the minister on drought assistance payments to farmers.

Mr Joyce has insisted he had no knowledge that his staff had inserted clarifying lines into Hansard but shadow agriculture spokesman Joel Fitzgibbon has been pursuing the matter through freedom of information channels, including seeking correspondence between the minister's office and the department.