More than 70% of A&E patients have to wait longer than the HSE's target time of six hours to be admitted to hospital and 4% have to wait 48 hours or more.
It comes after University Hospital Limerick recorded its highest-ever trolley figures last month.
Earlier in April, Tony Fitzpatrick, director of industrial relations with the Irish Nurses and Midwives Organisation, said hospital waiting times and assaults on healthcare workers are often linked.
On average, patients at Galway University Hospital, Cork University Hospital (CUH) and University Hospital Limerick (UHL) had to wait the longest to be admitted to other hospital wards.
38.4% of patients waited longer than 24 hours at Galway University Hospital, while 28.5% and 28% waited longer than one day to be admitted at CUH and UHL respectively.
For the survey from the Health Information and Quality Authority (Hiqa) and HSE's 2021 Inpatient Survey, 10,743 patients were asked about their experiences of treatment in 40 hospitals around the country in the last year.
Among the other areas cited by patients as "needing improvement" were emotional support, having sufficient time to discuss care and treatment options with a doctor, information on how to manage a condition after leaving hospital, and the opportunity for family members and friends to talk to a doctor.
Patients at smaller and more specialist hospitals tended to report more positive experiences compared with medium and large hospitals.
The report differs from those carried out in previous years, given the impact the Covid-19 pandemic and the cyberattack on the HSE had on the health service in 2021. Indeed, last year's report was delayed from May to September as a result of the cyberattack.
In terms of Covid, the majority of the patients surveyed (68%), said they did not feel at risk of contracting the virus during their time in hospital. Conversely, 9% said they "definitely" felt at risk of catching Covid while being treated.
However, 12% said they could not find a member of staff to talk to about their worries or fears about it.
The results of the 2021 National Inpatient Experience Survey were launched this morning by Minister for Health, Stephen Donnelly TD. Find out more at https://t.co/2td0DhzeUV, @CareExperience or watch our animation at https://t.co/bmEICcoBVr pic.twitter.com/5vpeQbFPcS— HIQA (@HIQA) May 9, 2022
Despite lengthy wait times, the survey found that most patients had positive interactions with hospital staff last year, with 83% rating their hospital experience as good or very good.
Most patients stated that hospital staff treated them with dignity in emergency departments, provided them with privacy while being treated or examined, gave clear answers to their questions, assisted them with controlling their pain, and helped them to get to the bathroom, if needed.
81% of the patients surveyed said they "always" had confidence and trust in the hospital staff who treated them.
Speaking this morning, Health Minister Stephen Donnelly said it was encouraging to see that patients were continuing to have positive interactions with nurses and doctors.
“The survey findings also highlight that there is still room for improvement, and it is absolutely essential the health service listens and responds when patients share their experience," he said.
Hiqa CEO, Angela Fitzgerald, said the report's findings underlined "how important it is to patients, and their family members, to have opportunities to talk to healthcare staff, to ask questions and to share their worries."
She said Hiqa would be focusing on these areas in 2022.
HSE CEO Paul Reid said the health service "must now learn from and act on the survey findings regarding long waiting times in emergency departments, limited emotional supports, the need for more information about managing a condition at home, and for opportunities for family members to talk to clinicians.
"We will use the findings to continue to develop and implement quality improvement initiatives to improve the experience for patients," he said.