The IFA has insisted that association president Eddie Downey and the organisation's powerful executive board had "carefully considered" the correspondence from Con Lucey and addressed the issues raised.
Mr Lucey dramatically resigned as chairman for the IFA's audit committee recently, sparking serious unease among senior elected members of the association.
It is believed Mr Lucey's resignation followed his expression of concerns about the independence of the audit committee.
In an IFA statement to Farming Independent it was accepted that "a lack of direct communications" between the IFA general secretary Pat Smith and Con Lucey had led "to genuine misunderstandings, which were unhelpful."
"In his correspondence to the [IFA] president, Con Lucey made a number of procedural recommendations to strengthen the new audit committee and these have been agreed by the IFA board," the IFA stated.
"Con Lucey was strongly of the opinion that the chair of the committee should be external to the association and have auditing/accountancy experience. This has also been agreed and the IFA president is in the process of securing an external chairman with the appropriate experience. The work and recommendations of the audit committee will be brought to the executive board and the committee will also report to the executive council," the statement added.
Mr Lucey also highlighted the need to establish an independent remuneration committee to establish the pay and benefits package for the general secretary of the association. and to set the financial compensation the IFA president receives during his four-year term.
Important changes to the accountancy standards in Ireland, which come into force next January, will require the annual accounts of organisations such as the IFA to set out the remuneration of key management.
In his correspondence, Mr Lucey was critical of what he claimed was a lack of accountability in setting the remuneration of the president and the general secretary, the most senior officers in the IFA. He said an independent remuneration committee would bring greater transparency to the process.
But the IFA pointed out the pay package for the IFA general secretary was reviewed annually by a remuneration committee made up of the [IFA] president and national treasurer, and any decisions made are signed off by both of them with the association's financial controller.
"The association confirms that its financial procedures are robust and that the day-to-day affairs are carefully managed by the financial controller, with final sign-off on all expenditures by the elected national treasurer. The association's financial affairs are independently audited by Deloitte each year," the IFA statement added.
IFA was asked by Farming Independent to furnish details of the secretary general's pay and benefits package, and also the level of compensation paid to the IFA president annually, but no answer to these questions was received.