The secretary of the Department of Agriculture, Dr Paul Grimes, has gone on unexpected leave after requesting an extraordinary Senate committee hearing in order to provide “highly pertinent” information about a long-running saga over changes to the official Hansard record of answers given by his minister, Barnaby Joyce.

At the heart of the controversy is Joyce’s insistence to the parliament that corrections to the Hansard record of an incorrect answer he gave regarding drought support loans on 20 October had been made by his staff, without his knowledge, and that he had asked for the changes to be reversed when he became aware that they had been made.

The opposition agriculture spokesman, Joel Fitzgibbon, has been questioning whether Joyce did know about, or request, the changes – an allegation which, if proven, would mean Joyce had committed the sackable offence of misleading the House of Representatives.

Fitzgibbon has made freedom of information requests for information and documents relating to the process of changing the Hansard, and Grimes’ “highly pertinent” information related to documents not provided as a result of those requests.

Staff in the Department of Agriculture were advised Grimes had gone on leave on Friday afternoon, without usual information about the duration of his absence. Government and departmental sources said the leave was “unexpected”.

In the letter to the committee chair, obtained by Guardian Australia, Grimes wrote that he had suspected at least one document had not been provided as a result of the FOI request and that he also had “further relevant information”.

“Subsequent actions (in particular, the tabling of the document by the minister in the house of representatives on Tuesday 24 February) and my further inquiries within the department, including new information my officers had not previously provided to me and a telephone call with the minister’s chief of staff, have confirmed by concerns to have been correct,” Grimes wrote on 2 March.

“Without my intervention I considered there was great danger of the committee being inadvertently misled as to the existence of such a document, which it now seems was never released under FOI.

“I have further relevant information that would, I believe, be highly pertinent to the committee’s consideration of the broad context in which I considered that the further evidence I provided was necessary.”

But when the committee reconvened last Wednesday as a result of Grimes’s request – with a much larger turnout of Coalition senators than normal – Grimes did not provide significant new evidence. Some of the committee’s questions were taken on notice, meaning written answers will be provided by mid-April.

During that hearing, Labor’s Doug Cameron, questioning Grimes and indicating that he was reading from Grimes’s letter to the committee chair, said: “But you do also go on to indicate, ‘I have further relevant information that would, I believe, be highly pertinent to the committee’s consideration of the broad context in which I considered that the further evidence I provided was necessary.’ Then you say, ‘This includes specific information relating to the original alterations made to Hansard and the multiple actions I took personally at the time to seek rectification, including a personal meeting with the minister before the alterations became public.’”

Fitzgibbon told Guardian Australia he was still looking for answers.

“I want assurances the minister hasn’t misled the house. I am also concerned about how he misled the farming community with his original answer and that then the Hansard record was doctored ... I find it hard to believe such extensive changes could be made without his involvement or knowledge,” Fitzgibbon said.

“The minister and his office did everything they could to frustrate the FOI process and I remain concerned that documents may be outstanding.”

But Joyce said last week Fitzgibbon had “been going around, talking about some grand conspiracy”.

“[Fitzgibbon] talks about it as if it’s Watergate; he talks about it as if it’s the extra gunman from the grassy knoll; he talks about it as if it’s the riddle of the Enigma machine. And then after the issue has been dealt with in the chamber, has been talked about during Senate estimates, has been investigated by the speaker of the house and has an extra Senate inquiry today – what have we got? Nothing. I don’t know what on earth [Fitzgibbon] is banging on about.

A spokesman for Joyce said on Monday “personal leave arrangements are not the minister’s business. They are not the journo’s either. The minister has a strong working relationship with his department”.

The Department of Agriculture said that “the secretary, Paul Grimes, is currently on leave. The department does not comment on an individual’s leave arrangements”. Grimes declined to comment.

Tony Abbott’s statement on ministerial standards provides that, “ministers are expected to be honest in the conduct of public office and take all reasonable steps to ensure that they do not mislead the public or the parliament. It is a minister’s personal responsibility to ensure that any error or misconception in relation to such a matter is corrected or clarified, as soon as practicable and in a manner appropriate to the issues and interests involved.”

Grimes is a long-serving and respected public servant. He was previously the secretary of the Department of Sustainability, Environment, Water, Population and Communities.

Timeline of events

20 October 2014 – Barnaby Joyce answers original question on drought support loans during question time

22 October 2014 – Joyce provides “additional information” to his original answer, but does not correct Hansard.

27 October 2014 – Joel Fitzgibbon asks Joyce about the differences between his answer and what was recorded in Hansard.

27 October 2014 (after question time) – Joyce emails letter to Hansard asking for the changes to be removed from the record of his original question on 20 October 2014. He returns to the parliament to say his staff changed Hansard without his knowledge. “On 20 October 2014 I understand a request for minor edits was made to Hansard by my staff without my knowledge. My staff have been counselled. Consistent with standing orders, I have asked that the changes requested by my office be removed from the Hansard before the Hansard is finalised.”