There were 704 patients in hospitals waiting for admission to a bed this morning, according to the Irish Nurses and Midwives Organisation.
The hospitals worst affected are University Hospital Limerick with 105 patients waiting, Cork University Hospital with 68 patients waiting, Tallaght University Hospital with 51 patients waiting and Sligo University Hospital with 44.
The high overcrowding comes after the May Bank Holiday weekend.
INMO General Secretary Phil Ní Sheaghdha said the service was seeing yet another predictable post-bank holiday surge in hospital overcrowding.
She said that of the five bank holidays so far this year, the service has seen out of control numbers of patients on trolleys in the days following.
"This level of overcrowding must not be allowed to continue further into the year. Senior decision makers in both the HSE and Government must come together now to develop a year-round plan to tackle this crisis," she added.
Overcrowding crisis: Why is the problem not yet fixed?
The HSE said that each hospital group implemented plans to alleviate overcrowding in their hospital EDs over the bank holiday weekend, adding that hospital and community teams continue to work closely to identify patients suitable for discharge home, to community beds or to private facilities in order to maximise the number of beds available in acute hospitals.
In a statement this afternoon, the HSE said that it "regrets that patients, particularly those who are non-urgent, may expect to experience long waiting times".
"Hospitals and our staff are working hard to do all they can to reduce the length of time patients wait in EDs."
It added that EDs will continue to see and treat patients who require urgent and emergency treatment first.
People should continue to consider all options and pathways available to them before attending an ED – Injury Units, GP Out of Hours, GPs and community pharmacy, it added.
Meanwhile, the HSE Chief Executive, Bernard Gloster said the health service is moving away from traditional Winter planning and will instead take an all-year round approach to managing emergency department capacity.
He said that a plan for the remainder of this year will be finalised this month and each hospital group and community healthcare organisation will report to him on the detail of the approach in each area.
Mr Gloster said the initiatives will not end the pressures but will help the HSE manage them to the best extent possible, reducing public discomfort and improving the working environment of staff.