The Taoiseach says the Mother and Baby Homes report highlights a "dark, difficult and shameful" chapter in Ireland's history.
The Commission of Investigation has found 9 thousand children died in the 18 institutions examined, including The Castle, Newtowncunningham and The Stranorlar County Home - around 15% of all those born.
56,000 unmarried mothers - ranging in age from 12 years old to women in their 40s - passed through the homes between 1922 and 1998.
The Commission's found their cruel treatment and stigmatisation was supported and condoned by church and state.
Following its recommendations, a redress scheme is to be set up and legislation will be brought forward so survivors can access their birth information.
The Commission of Investigation has deemed The Castle, Newtowncunningham a non-traditional mother and baby home, rather a hostel.
325 women from across Ireland and Northern Ireland, accompanied by 64 children passed through its doors between 1982 and 1998.
Five babies born to mothers at The Castle died in hospitals shortly after birth.
The Commission of Investigation also looked at the Stranorlar County Home where 1,646 unmarried mothers and 1,777 children lived between 1922 and 1964.
Conditions there have been described as 'very poor'.
In the early 1920s, it was overcrowded with inadequate water and sanitary services including; no hot water in the operating theatre, as a result there were several outbreaks of typhoid.
Most residents had to use outdoor toilets that were described as 'bad or rather revolting'.
Admissions to its labour ward were discontinued in 1935 as it lacked a bathroom and running water.
At one stage, the Minister for Local Government ordered the home to supply residents with 3 meals a day as opposed to 4.
Most of the work at the home was carried out by unmarried mothers, who were unpaid.
Mothers of older children lived and slept separately and saw each other only on Sundays.
Institutional records of Stranorlar county home suggest 343 'illegitimate' children born in or admitted to the institution died in infancy or early childhood. Cross reference of records held by the GRO confirmed 339 child deaths - 60% of deaths were attributed to pneumonia or bronchitis.
The full report can be accessed here.