The apology by CURA, run by the Irish Catholic Bishops Conference, is published in the latest edition of the Irish Catholic.
It ends a four-year wait for justice by three volunteers at its Letterkenny Centre in Donegal.
The volunteers, Phil Murray, Mary Kelly and Ann Farren, were expelled from CURA in May 2005 after raising concerns about the Positive Options Leaflet.
The following month the counselling service stopped distributing the pamphlet.
The leaflet is published by the Crisis Pregnancy Agency (CPA) that funds pregnancy counselling agencies.
In November 2007, the CPA confirmed CURA was to get more than €2 million in state funding after a settlement had been reached in the long-running row over abortion information.
It was agreed that, instead of referring women still undecided about their crisis pregnancies to agencies providing abortion information, CURA would refer such women to their GP or provide them with a list of GPs drawn up by the Health Service Executive.
The CURA apology states: “The National Executive Council of CURA is pleased to announce that agreement has been reached with Phil Murray, Mary Kelly and Ann Farren, three volunteers at the Letterkenny Centre.
“The volunteers have been reinstated as members of CURA and have now resumed functions on behalf of CURA.
“CURA wishes to apologise to each of the volunteers for the distress caused to them and looks forward with gratitude to their continuing commitment to the work of this organisation.”
Spokesperson for the bishops, Martin Long, said he had nothing further to add to the apology.
Seamus Farren, whose wife, Ann, was one of the four women expelled, was delighted their stance had been vindicated at long last.
“It has been a long road for them,” he said.
The women, he said, had been reinstated a year ago and were happy to be back working for CURA, but had been insisting on the apology because they had been publicly expelled from the agency.
Mr Farren said he personally could not see why CURA had to be linked to the CPA.
“CURA should not have to be funded by the CPA – the bishops should take responsibility for it themselves,” he said.
Irish Catholic managing editor Garry O’Sullivan said the Catholic Church still had a long way to go to reach something close to openness and transparency.
“For four years this paper has highlighted the case of the CURA 4 and not once in those four years has the CURA leadership answered any questions,” he said.