Chief Executive Officer of Console Paul Kelly has resigned and the board of the charity has set up an independent external review of issues raised in a report by the RTÉ Investigations Unit.
Patricia Kelly, Mr Kelly's wife, and Joan McKenna, Mr Kelly's sister, have also resigned as directors of the charity.
A statement issued on behalf of Console confirmed the resignations. It said the board is appointing external reviewers to appoint a review of the issues that were raised in the RTÉ report.
The reviewers are Tom Murray, Forensic Accountant and David Hall. The statement said they will be provided with "full and unrestricted access to Console's premises, staff, files and records."
The reviewers have been asked to "furnish to the Board [of Console] a report of their findings and recommendations within 60 days."
The report by the RTÉ Investigations Unit revealed serious mismanagement and deception by Mr Kelly, who was the founder of Console Suicide Bereavement Counselling Limited.
"RTÉ Investigates - Broken Trust" - revealed concerns surrounding the charity's finances with regards to cash receipting, expense claims and financial accounts.
The report also showed that, when applying for State grants, the charity on several occasions altered accounts to omit the reference to directors' pay and other benefits.
These amounts totalled over €215,000, according to accounts filed by Console with the Companies Registration Office for the three years 2010 to 2012.
There are very strict rules in place for organisations like Console that avail of the tax exemption status from the Revenue Commissioners, notably independence of the board of directors and no payment of salary to directors. If a charity does not comply its tax exemption status can be withdrawn.
Console currently avails of the tax exemption therefore the payments made to the directors from 2010 to 2012 were not permitted under Revenue regulations.
The payments were also prohibited under the company’s Memorandum of Association. Furthermore, in accounts seen by the RTÉ Investigations Unit submitted to funders, references to directors' pay and other benefits were omitted or edited.
There were other misrepresentations. The directors in the period 2010 to early 2014 were made up of Mr Kelly, his wife Patricia, another close family relative and, for a brief period, a second member of his immediate family.
Once again under the rules of the Revenue Commissioners, there should be "a minimum of three Officers, Trustees or Directors, who are not related and (are) independent of each other."
However, when Console submitted accounts to funding agencies such as the Department of Foreign Affairs or the Health Service Executive, Patricia Kelly signed the accounts using her maiden name Patricia Dowling, making it less apparent that the directors were not independent of one another.
In other company documents, directors who were members of the Kelly family were registered with varying dates of birth.
In documents submitted to funders, the charity also incorrectly claimed that certain people were board members.
One of these was former senator Jillian van Turnhout who told the programme that she was "stunned" that her name had been used and that it is "hugely alarming that any charity would purport that anyone is on the board who is not on their board."
Ms van Turnhout’s name appeared on a list that included at least five other directors whose names were used without their permission.
In an interview for the programme, HSE National Director for Mental Health Anne O'Connor confirmed the HSE has concerns arising from an audit it conducted on the charity.
The audit examined "the governance of Console in terms of its structure, its management and the actual financial arrangements within the organisation in terms of cash receipting, expenses and accounts," Ms O’Connor told RTÉ.
"There are a number of concerns within the report," she said, adding that it is in final draft form and contains 229 pages and 89 recommendations. When pressed she said she could not comment on the specific findings.
The audit was commenced in April 2015 on foot of concerns raised by the HSE’s National Office of Suicide Prevention.
Ms O'Connor said "the office couldn't be satisfied that ... the information we were getting was something that we could live with or that fitted with the governance framework set out in the formal agreement" with Console.
The HSE is Console's main funder: providing over a quarter of the charity's income of €12m in the nine years to 2014.
Ms O'Connor said that audit dealt only with finance and governance issues and does not relate to the counselling service that Console provides.
"At no time during this process have we had concerns raised in respect of the service that is provided to the public," she said.
The RTÉ Investigations Unit report follows a document trail evidencing many examples of misrepresentation by the charity and also highlights Paul Kelly’s controversial involvement in the charity sector going back three decades.
In correspondence to RTÉ, Mr Kelly has denied any wrongdoing.
The gardaí has said it has recently received correspondence in relation to a particular charity regarding a number of issues.
In a statement, it said the issues are being assessed to determine if there are criminal matters which fall within the remit of An Garda Síochána.