Almost 70% of patients waited more than the 6 hour target to be admitted to hospital this year.
A new survey by the HSE has also revealed that 84% said their hospital stay was good or very good.
Over 14,000 people responded to the first patient experience survey after being admitted to hospital in May and the results will be used to improve the quality and safety of services in the future.
Rachel Flynn from HIQA says one of the first things they need to tackle is waiting times.
She said: "The survey results clearly indicate that we are not reaching our target around emergency department waiting times - we have fallen short of those targets which we set within the HSE.
"They are an indication that we need to look at this again to see where the problem is - none of the hospitals reached the target where 95% of patients should wait less than 6 hours."
49% of patients also said that they could not always find a member of staff to talk to about their worries or fears and 36% said that they were not involved as much as they would have liked to be in the decisions about their care.
However, 83% of people said that they always had confidence and trust in the hospital staff that treated them.
The results of this National Patient Experience Survey was launched today by An Taoiseach Leo Varadkar TD and Minister for Health Simon Harris TD in Dublin.