The Office of the Ombudsmen says the majority of complaints it received in 2011 were against the Department of Corrections.
It says there were nearly 3940 complaints - most of them from prisoners or on their behalf.
The most common complaints relate to prisoner property, then phone calls and written communications, prisoner transfers, health services and general conditions.
The office is also directly involved in monitoring deaths in custody.
Last year, there were 23 deaths, compared with 15 in 2009, and 16 in 2008.
The Office of the Ombudsmen says in 83% of cases, it concluded it found the department's investigation to be fully satisfactory.
The remaining 17% were mainly satisfactory, but the Ombudsman made additional comments on the reports.
