The Department of Justice and the Ombudsman are at odds over the administration of a scheme designed to compensate women who were admitted to or worked in institutions and Magdalene laundries.
The differences centre on why some women were excluded from compensation under the Magdalene Restorative Justice Scheme, which was set up in 2013.
In a report due to be published today, called Opportunity Lost - An Investigation by the Ombudsman in to the administration of the Magdalene Restorative Justice Scheme, the Ombudsman Peter Tyndall criticises the Department of Justice for its administration of the scheme and recommends the cases of women omitted from it be re-examined.
The Ombudsman's investigation was prompted by complaints by a group of women who were excluded from the scheme.
The department omitted the women from the scheme because it said they were not in one of the 12 institutions covered by it.
In the report, the Ombudsman rejects this saying evidence from his investigation shows some of the Magdalene laundries were inextricably linked with other units, attached to the laundries, or located on the same grounds. He said they should be considered to be one and the same institution.
Mr Tyndall recommends the department to re-examine the cases of women excluded from the scheme and to report back to him in three months.
He also expresses frustration over the failure of discussions between his office and the department to resolve the complaints.
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"I was married to my husband for ten years before I told him my story. I was that ashamed. I was so ashamed."
The Ombudsman describes a failure by the department to put in place requirements for women, without the capacity to make decisions on their own behalf, to make applications to the restorative scheme as "maladministration".
In a submission also published in the Ombudsman's report, the secretary general of the department says the Ombudsman's criticisms derive from the belief there was a restricted interpretation of the scheme.
The secretary general adds he cannot agree with the Ombudsman's interpretation.
The Ombudsman's main recommendation, he contends, would "involve double payments, as persons in industrial schools have had a separate compensation scheme" and "would involve a very significant increase in the number of potential applicants way beyond the number envisaged by the Government when the scheme was approved".
"This amounts to a major change in the scope of the scheme which only the Government can decide upon", the secretary general adds.
Minister for Justice Charlie Flanagan said his department would give "full and careful consideration" to all the recommendations in the Ombudsman's report.