Disability charity Rehab is to undertake a root-and-branch review of its operations in light of the row over executive pay and links to government lobbyists.
The board of the not-for-profit organisation admitted its reputation had been damaged and said it was trying to deal with the controversies openly as it fights to stave off a funding backlash.
Former boss Angela Kerins quit last month - walking away from a 250,000 euro a year pay cheque - following a protracted dispute about the reluctance to divulge her wages.
There were also concerns about the operation of Rehab's lottery scratch card scheme which barely turns a profit, and the role and influence of Fine Gael strategist and former chief executive Frank Flannery, who quit last month over a suggested conflict of interest.
Rehab chairman Brian Kerr sent a message to staff today in which he accepted the response to the political and public demands for information had been inadequate.
"We recognise that as a board we have not exercised strict and appropriate oversight of certain issues which have come to public attention in recent weeks," he said.
"The board's priority now is to initiate a programme of transformation and change which will allow us to candidly confront the issues before us and to rebuild the reputation, staff morale and effectiveness of the organisation."
Mr Kerr said Rehab wanted to rebuild confidence in the organisation and the trust of the people who use its services, staff, and the people who donate and fund their work.
He also acknowledged that colleagues in the charity sector were suffering as a result of the lack of transparency at Rehab.
Mr Kerr said: "As a matter of urgency, we are committed to making whatever changes are necessary, including changes to the board, to ensure that the organisation can have the full confidence of those who use our services and those who fund us."
Eddie Molloy, a change management consultant and former charity boss, will lead a review of the governance and structures of the Rehab Group and how it conducts its affairs.
The review will examine possible changes to the board and how it works to ensure the right skills and procedures are in place for quality oversight and how to increase transparency about Rehab's work and how staff are paid.
It will also look at how the group is structured with new charity regulations on the way and how the board upholds Rehab's core values.
Mr Kerr said: "The Rehab Group has a proud record of service. We have helped to make lives better for many people; over the last decade the organisation has grown and developed new and innovative services, supporting many thousands of people.
"Our reputation has been seriously damaged but by candidly confronting these issues once and for all and implementing the right transformation programme, we can emerge a stronger and better organisation."
Depsite resigning, Ms Kerins and Mr Flannery are expected to agree to attend the next sitting of the Public Accounts Committee as it continues to examine spending at Rehab.
February was the first time salary details for the Rehab chief were released since 2011. It is not clear what 56-year-old Ms Kerins' pension arrangements are.
The organisation gets about 83 million euro a year in public funds.
The Public Accounts Committee is pursuing Rehab over Ms Kerins' wages and the pay of 12 executives who were on 100,000 euro or more a year, and also information on contracts signed with companies with links to senior figures in the charity.
Rehab says it is an independent international group of charities and commercial companies with more than 3,500 staff involved in health and social care, training and education, rehabilitation, employment and commercial services in Ireland, England, Wales, Scotland, the Netherlands, Poland and Saudi Arabia.
It had a turnover of 183 million euro in 2012.
Chairman of the Public Accounts Committee John McGuinness said the review was an important first step.
"We will consider in detail the changes necessary to ensure there is adequate transparency, accountability and oversight at Rehab," he said.
Ms Kerins and Mr Flannery had not replied to invites from the committee to attend but Mr McGuinness said they are expected to come back for questioning.
Mary Lou McDonald, Sinn Fein deputy leader, said whether they do will be the first test of sincerity.
She added: "That is what the public interest demands, and nothing less will do."