A survey by Criminal Justice Inspection found 80% of prison officers were Protestants and Catholic inmates receive less favourable treatment.
This inspection examined whether criminal justice agencies were meeting their legal obligation to ensure equality and human rights are promoted.
The Prison Service was strongly criticised in the report.
Prison Service director Robin Masefield said they had no control over the religious backgrounds of people sent to jail.
“In the past number of years, we have had a higher proportion of Roman Catholics coming through, particularly on the remand side, so inevitably one’s getting something of a slight disproportionate make-up there,” he told the BBC.
The majority of prison wardens in Northern Ireland have historically been Protestant, and Mr Masefield said about 25% to 30% of recent applicants to the Prison Service were Catholic, something which was “not as high as the police but a step in the right direction”.
Mr Masefield said the Prison Service did not have 50-50 recruitment provisions like the police, but they had “made great strides in the recent past” and aimed to achieve a target of 35% Catholic applicants by 2011.
The report, published on Tuesday, looked at equality and human rights in every aspect of agencies’ operation, policies and practice.
BBC NI Home Affairs correspondent Vincent Kearney said: “Inspectors found that Catholic prisoners received fewer privileges than Protestants and the report calls on the prison service to investigate why this is the case.
“But the inspectors also criticise other agencies for failing to comply with their legal obligation to properly collect and monitor equality information.”
The report’s authors said there wasn’t enough information about how the criminal justice system treats defendants, victims or witnesses.
Dr Michael Maguire, Chief Inspector of Criminal Justice in Northern Ireland, said: “The report highlights the importance of collecting timely, relevant and comprehensive information.”
He added: “There is a question to be answered as to why the religion of a prisoner would have an impact on the regime that they experience within the Prison Service.”
Privileges for prisoners include telephone access, television-watching and association with other inmates.
Prison Service equality adviser Monica Fitzpatrick said although she did not dispute the figures contained in the report, the proportion of prisoners from different religious backgrounds was constantly fluctuating.
“The important thing about equality monitoring is that you do not take raw data without context and draw conclusions from that,” she said.
Criminal Justice Minister Paul Goggins welcomed the report and said the criminal justice system was committed to equality.
He said two of CJI‘s recommendations were already in place and an action plan for the others had been drawn up.
The report was also welcomed by the Equality Commission for Northern Ireland. Chief Executive Evelyn Collins said: “Effective monitoring allows public bodies to identify and address any underlying issues which may impact on the promotion of equality.”
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