A number of religious organisations have apologised for their role in operating the Mother and Baby Homes.
A research report into operation of the institutions, published on Tuesday, examined eight mother and baby homes, a number of former workhouses and four Magdalene laundries.
Some of those investigated were operated by the Presbyterian Church.
Moderator of the Presbyterian Church in Ireland Right Rev Dr David Bruce said: “We deeply regret and unreservedly apologise for the damaging effects of institutional care, in which the Presbyterian Church in Ireland, or its members, played a part.
“We pray that those who still live with the memories of those days will know and experience the peace of God which may only be found in Christ’s love.”
Rev Bruce said the facts uncovered in the newly-published report “make for deeply uncomfortable reading”.
He added: “The terrible cost to every mother and child who suffered in such institutions is upsetting for all of us in society.
“The report sheds much-needed light on a dark era in Northern Ireland’s history and speaks more of the inhumanity shown to mothers and their babies and their wider families at that time, than the Christian care and compassion they deserved.
“In any forthcoming inquiry, or process, we will certainly co-operate as far as we are able.”
A Church of Ireland spokesperson said the publication of the research report on Mother and Baby Homes and Magdalene laundries in Northern Ireland “sheds further light on the suffering of women and children in relation to their experiences in these homes”.
“The Church of Ireland will be giving the report further careful consideration, as it has done with the recent report in the Republic of Ireland,” they said.
The Sisters of Our Lady of Charity of the Good Shepherd, a Catholic religious order, have said they will provide their “fullest co-operation” with the investigation arising from the Mother and Baby Homes report.
The Order of nuns said they “deeply regret that we could not and did not always meet the multi-faceted needs of these women” who entered their homes.
The Order ran a number of homes in Derry, Belfast and Newry.
In a statement, they said: “This was not a good experience for everyone and we wish that we could have done more for the women in our care at such a critical time in their lives.
“We deeply regret that we could not and did not always meet the multi-faceted needs of these women.
“We will need more time to review the contents of the report in detail and we will affording the independent investigation, announced this evening, our fullest co-operation.”
More than 10,500 women entered mother and baby homes over a 68-year period from 1922.