Only around 200 of more than 4,000 charities required to register with the Charities Regulatory Authority have done so, despite the threat of stiff fines for non-compliance.
The widespread failure was revealed by Minister for Justice Frances Fitzgerald as she announced a 12-month extension of the deadline.
It risks undermining confidence in a sector that has been working to regain public trust after the Central Remedial Clinic scandal of 18 months ago.
The Irish Charities Tax Reform group (ICTR) today expressed concern that the announcement of an extension of the registration deadline for certain charities risks undermining confidence in the sector which has been trying to regain public trust since the CRC scandal.
A spokesperson for the ICTR group told RTÉ News it was "over-ambitious" of the 2009 Charities Act to set a deadline of six months for charities which were not already registered with the Revenue Commissioners to register with the new Charities Regulatory Authority.
Minister Fitzgerald said the move does not affect 8,500 other charities that have been automatically registered with the CRA by virtue of the charitable tax status granted to them by the Revenue Commissioners before the establishment of the authority.
The CRA was established by the Government last October.
It came almost a year after a series of financial scandals at the CRC involving a gold-plated pension for its retired chief executive Paul Kiely, top-up payments to some executives and cross-directorships with a related company.
This and subsequent revelations about finances at the Rehab organisation led to a significant decline in public donations to most Irish charities.
In her statement this morning, Minister Fitzgerald emphasised that she had extended the deadline after consulting the CRA.
It was established last year under the Charities Act 2009 after a five-year delay spanning the terms of both the current and previous coalition governments.
The act says the first function of the CRA is to "increase public trust and confidence in the management and administration of charitable trusts and charitable organisations".
Minister Fitzgerald said: "It is important that all charities operating here meet their obligation to register on the new public Register of Charities.
"This register is intended to provide much needed additional transparency about our charity sector.
"I encourage any charity that was established before last October and that has not yet begun the registration process to do so now."
Greater support and awareness needed for CRA registration' - The Wheel
Ivan Cooper, Director of Advocacy at The Wheel, said many of the mostly smaller organisations concerned seem to be unaware of their obligation to register with the Charities Regulatory Authority
The Wheel also called on Ms Fitzgerald's Department of Justice and Equality to ensure that the Charities Regulatory Authority (CRA) is sufficiently resourced to communicate with, educate and support charitable organisations that have yet to apply to it for registration.
Mr Cooper also called on the Department to ensure that the CRA is given enough resources to support the other nine thousand or so registered charities that are currently completing their entry in the CRA's Register.
The Wheel is a national umbrella body that represents 1,100 charities here.
Mr Cooper said it will be working closely with the CRA and other partners in the charity sector to raise awareness of the requirements facing unregistered charities.
Applications for inclusion on the Register of Charities can be made through the website of the Charities Regulatory Authority at www.charitiesregulatoryauthority.ie