A survey of 1,200 in-patients has highlighted problems with emergency department conditions and waiting times.
The survey also highlighted issues with a lack of information about hospital routines and tests, medication side effects and aftercare following discharge.
The 2011 National Acute Inpatient Study for the Irish Society for Quality & Safety in Healthcare (ISQSH) shows that 65% of respondents were unaware of the complaints procedure in the hospital.
It found that 18% wanted to make a complaint but over a third of those did not do so, with many feeling they did not have the opportunity.
The Society said this means that based on 350,000 patients discharged in 2011, around 63,000 wanted to discuss an area of dissatisfaction and a third of these may never have had the opportunity.
Of those who underwent a procedure, 52% said the doctor marked the site for surgery in advance.
The survey also showed that 93% of patients reported satisfaction with the service they received and 96% felt they were treated with dignity and respect.
A second survey on Compassion in Healthcare reveals that over one in three people believe the Irish system does not provide a compassionate service.
Most people expressed concern that the increased emphasis on controlling costs will decrease compassion in healthcare professionals.
The compassion survey was conducted last year and involved 236 past patients.
ISQSH chief executive Dr Hilary Dunne said this may be the last independent survey of patient experiences in Ireland as the Health Service Executive has terminated its research grant, leaving further patient experience surveys to be conducted by the Government and related bodies such as the HSE.
ISQSH said it has not been offered an opportunity to meet with Minister for Health James Reilly to discuss its call for the research grant to be reinstated.
Asked about the issue and the decision of the HSE to also cease funding the Irish Patients' Association, Mr Reilly thanked the organisations for their “sterling work to date”.
He said he was exploring new ways of more effective patient representation, including having patient champions in hospitals.
Mr Reilly was speaking at the 3rd National Patient Safety Conference in Dublin.