Four directors of the Pilgrim House Community, which is funded by the Health Service Executive, placed a half-page advertisement in the paper in which they apologised to the founder of the organisation, Helena O'Leary.
In the advertisement they apologised for the damage caused by their "dishonesty" to her seven years ago and for lying about their reasons for being part of the organisation.
The advert was signed by Bridget-Anne Ryan, Conleth J Finnegan, Claudia Carvajal M and Benedict Hogan, all of whom are directors of Pilgrim House.
Bridget Anne Ryan - a former editor of The Irish Catholic - said the apology had been made in a personal capacity by each of the signatories.
She declined to be drawn on what the apology related to except that the issue attracted misleading media coverage of the organisation and ended the spiritual community which existed within the organisation.
"I don't want to say anything else today which will distract from this. I have nothing else to say except that how deeply sorry I am," she said.
"The apology relates to the fact that the Pilgrim House Community no longer exists. It ended seven years ago. What exists now is an organisation which provides residential care for the intellectually disabled. The community life that was there is over."
Today Pilgrim House Community provides residential services to five intellectually disabled people near Celbridge, Co Kildare. It came to prominence seven years ago when one member of the community took her own life at the organisation's headquarters, then located at Inch, Co Wexford.
A coroner's court hearing in October 2001 concluded Margaret Foley Smith hanged herself after a violent row with her separated husband, who was also a member of the community.
However, members of Pilgrim House were later involved in handing out leaflets to Mass-goers in Ms Foley Smith's home parish in Co Meath, which contained groundless allegations of incest in her family.
A number of Masses in different parts of the country were also disrupted by members of Pilgrim House who were highlighting alleged cases of incest.
A Garda investigation took place into the incidents. However, no charges were brought.
When asked yesterday, none of the directors would comment on whether yesterday's apology was linked to these incidents.
Dialogue Ireland, an organisation which gathers information on new religious movements, says Pilgrim House has displayed cult-like characteristics and it has passed this information on to religious authorities.
The Health Service Executive yesterday confirmed it provides about €210,000 a year to Pilgrim House for providing a full-time residential service to five clients with intellectual disability.
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