The Dublin Region Homeless Executive (DRHE) has called for the dissolution of the Inner City Helping Homeless charity following allegations of sexual abuse.
In its statement, the DRHE said it was "absolutely shocked" and "distressed" at the allegations.
Gardaí are investigating complaints of sexual assault made by two men against the charity's founder and independent councillor Anthony Flynn, who was found dead last month.
There is only one board member left for the Inner City Helping Homeless charity following a series of resignations.
The charity gave two weeks' notice on Monday to the Office of the Director of Corporate Enforcement and the Charities Regulator that it intended to ask the High Court to appoint an inspector.
It is understood that there is at least €750,000 in bank accounts connected to the charity.
In a statement, the DRHE also called for more vetting for those working unofficially with the homeless.
"The DRHE is strongly of the view that greater regulation, vetting, and scrutiny is required for organisations/charities that set themselves up as service providers for homeless persons, including the provision of on-street food services.
"Several such organisations not funded by the DRHE have come into existence in recent years and the DRHE and our partner agencies will be endeavouring in the coming months to bring the necessary expanded scrutiny and regulation to all such organisations."
The statement added that the Inner City Helping Homeless charity was not funded by the DRHE.
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Speaking to RTÉ's News at One, Dublin City Council's deputy chief executive Brendan Kenny said that greater scrutiny of the charity sector is needed as he repeated calls for ICHH to be wound down quickly.
Mr Kenny, who also has responsibility for the DRHE in his role, described the allegations against Mr Flynn as "absolutely shocking".
He said that "as a result we think it's time for ICHH to be dissolved and wound up and we think that's what is going to happen in the near future and ... the quicker that happens the better".
Mr Kenny said the Executive is satisfied that the good services provided by ICHH can be transitioned and managed by other organisations.
He said that the situation for homeless people in Dublin has improved considerably in recent months and there are beds in the system for everyone who needs them.
Mr Kenny said the issues at the ICHH charity highlight the lack of regulation and scrutiny of many new charities that have been set-up in recent years without State funding.
He said that, in particular, there is a gap in the garda vetting system which is not required for those working with vulnerable adults in the homeless sector.
He said that many of these organisations "often do good work but in light of this we need more scrutiny, accountability and vetting and that is something we need to put in place over the coming months".
The DRHE has published contact numbers for sexual assault victims to seek help: Support Service for Victims 087 326 6630, Rape Crisis Centre 1800 778 888, Homeless Freephone 1800 707 707.