The groups have described the commission’s decision as a waste of resources.
The Dublin Commission of Investigation had collected material on a total of 102 priests but selected a sample of 46 to complete their report.
The files scheduled to be destroyed are those relating to the remaining 56 priests whose cases were not explored.
Commission barrister Ita Mangan confirmed files on the remaining priests would be "gotten rid of" or "shredded".
Rape victim support groups are now calling for the unexamined files to be retained and investigated further.
During its three-year-inquiry, the Dublin Archdiocese Commission of Investigation collected files from the Church, gardaí and the health authorities in relation to 172 named and 11 unnamed priests.
After concluding that 102 of the those priests were within its remit, it chose a representative sample of 46 priests.
The commission told the Irish Examiner yesterday that files on the sample group of priests would be given over to the national archives.
Files on the remaining priests would be destroyed as they had not been fully investigated.
Said Ms Mangan: "We had 46 priests out of 102, so we have some documentation about those [others] but that won’t be going into the archives because they weren’t investigated.
"The object of this commission was never to establish whether or not there was actual child sex abuse, we were only specified to look into the handling of the abuse and we were asked for a representative sample. We would be here for another three years if we investigated the rest of them."
However, support group One in Four last night suggested the files should be retained and made available for further investigation rather than destroyed.
Executive director Maeve Lewis said: "What would disturb me would be if destroying those documents were to impede a criminal investigation into individual priests who may still be alive."
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