Chief Scout of Scouting Ireland Christy McCann is to step aside pending the completion of an independent investigation into the organisation's handling of an allegation of rape.
The case involved an alleged assault on an adult volunteer by another adult volunteer.
Gardaí investigated the alleged assault but did not press any charges. The man was reinstated in the scouts and later promoted.
Minister for Children and Youth Affairs Katherine Zappone wrote to Scouting Ireland on Friday to advise it that she would be withholding funding from the organisation.
In the Dáil this afternoon, she confirmed that Mr McCann would step aside as she answered questions from Fianna Fáil TD Anne Rabbitte and Labour TD Seán Sherlock about what processes are in place for funding to be reinstated.
Minister Zappone said that she decided to withhold any further draw-down of funding to Scouting Ireland until such time as "I can be satisfied that the organisation's governance standards are up to the required level".
"As of now, I am not satisfied. And I have a responsibility to children and I have a responsibility for the use of public monies," she added.
Chief Scout of Scouting Ireland Christy McCann to step aside, Minister Katherine Zappone tells Dáil. pic.twitter.com/TGJxOHGDpw— RTÉ News (@rtenews) April 19, 2018
"I have been informed that the chief scout will be stepping aside from this evening, pending the completion of the independent investigation and the treasurer will serve as acting chair of the board in his absence."
Ms Zappone also said that: "Since the news broke, I've received other confidential correspondence from individuals in Scouting Ireland about additional matters of grave and serious concern.
"I will raise these issues with Scouting Ireland as part of the process."
This evening, Ms Zappone said work needed to be done for Scouting Ireland to provide her with the proper assurances that it has very good governance, as well as implementing high standards of child protection policies.
She said there were a lot of governance issues and the case that had been reported in the media indicated some of them. She also said that Scouting Ireland was funded up to the end of June.
Scouting Ireland commissioned safeguarding expert Ian Elliot to carry out a review into the case at the centre of this controversy.
Mr Elliot reported to the board of the organisation earlier this year. Scouting Ireland has also appointed a barrister to conduct an investigation into the handling of the case.