Prison authorities in the North destroyed 52,382 files in the months before the Freedom of Information Act was introduced.
The data included prisoner records, policy notes and medical logs and was disposed of before the January 2005 law making public bodies more transparent.
The Northern Ireland Prison Service has been criticised for destroying security files on hundreds of terrorist prisoners held at the Maze.
"It seems to me almost in contempt of the FOI Act and it is an extraordinary way to go about dealing with the new dispensation in relation to accessing documentation," said SDLP justice spokesman Alban Maginnis.
"It shows a very narrow and secretive attitude amongst the prison authorities and obviously it is regrettable that they stooped to such an excessive measure such as destroying a vast number of files."
An inquiry into the 1997 murder of LVF leader Billy Wright in the Maze Prison heard in November how 800 files with security information on terrorist prisoners released under the Good Friday Agreement had been shredded.
Wright, 37, was shot dead by three INLA gunmen on December 27, 1997, and Lord MacLean's inquiry is probing how the killers were able to target him in the high security centre.
Some of the material disposed of is uncontroversial and relates to medical and dental records. It is governed by a destruction timetable outlining the period which files have to be kept for.
The FOI was brought in to make public bodies more accountable but opposition politicians and campaigners have criticised shredding papers across government.
A Northern Ireland Association for the Care and Resettlement of Offenders representative said paperwork should be preserved.
"We would support people having access to information and transparency and with the Prisons Ombudsman and the review of criminal justice it is essential that this right is protected," Siobohan O'Dwyer from NIACRO said.
"We want prisoners to be able to access information and we support transparency in all government departments." The Prison Service said its actions were governed by official protocols.
"All of the files were destroyed in line with disposal schedules that were drawn up in consultation with PRONI.
"PRONI were also involved in the file review exercise which was in line with rules and regulations contained in the Public Records Act and the Section 46 Code of Practice on the Management of Records under the Freedom of Information Act 2000."
Inmates' files are normally destroyed six years after release.