Minister for Health Simon Harris has said "no effort or resource is being spared to improve the situation" in the health service where a record 656 patients were on trolleys or on wards waiting admission to a bed.
The figures were released by the Irish Nurses and Midwives’ Organisation.
The previous highest level of overcrowding was recorded on 3 January last year when 612 patients were waiting for a bed.
In a statement, Minister Harris said the health service is experiencing extra pressure because of the flu season.
He said while today's figures are very high and not acceptable, the Health Service Executive's trolleygar figures show the lowest trolley numbers for the first Tuesday in January in three years, which he said is a "modest improvement".
Unlike the INMO figures, the TrolleyGar figures do not give the number of patients placed on wards, who are waiting for admission for a bad, having already been admitted from an Emergency Department.
Consequently, the INMO figures tend to be higher.
The HSE/Department of Health TrolleyGar figures put the number of patients on trolleys at 457 at 8am.
The worst affected hospital today was St Luke's in Kilkenny with 57 patients waiting, followed by University Hospital Limerick 55, South Tipperary 45, Cork University Hospital 38 and Letterkenny 35.
The figures come as the INMO’s annual figures show that almost 100,000 people were waiting on a trolley or on a ward last year.
Mr Harris said that bed capacity will continue to be increased.
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Its trolley watch data shows there were 98,981 patients waiting last year, which is a 6% rise on the previous year.
University Hospital Limerick recorded the highest annual number of 8,869 patients.
Cork University Hospital recorded 6,815 patients waiting, while there were 6,563 recorded waiting at University Hospital Galway.
The Mater University Hospital in Dublin was the capital's most overcrowded hospital with 5,238 patients on trolleys during 2017.
The INMO says that its annual trolley watch figures indicate that any improvement in overcrowding is highly unlikely this year, unless drastic and innovative steps are taken immediately.
Phil Ni Sheaghdha, the newly-appointed general secretary of the union, said that on 28 and 29 December, 11 of the 29 hospitals used their full capacity protocol and placed extra patients on wards.
She said that under HSE policy, the joint chairpersons of the Emergency Department Task Force must be notified in advance of this.
Ms Ni Sheaghdha is one of the joint chairs and said that she was not notified. She said this was proof to demonstrate "an abandonment of the system for dealing with overcrowding".
The HSE's National Director for Emergency Management and National Ambulance Service said the health service has put in place a range of measures to deal with an increase in winter illnesses, including flu.
Speaking on RTÉ's News at One, Damien McCallion said the measures included the rescheduling of some elective surgeries and increasing the access of hospital patients to home care.
He said it was likely the flu season had not yet peaked.
Mr McCallion said there had been a drop in trolley numbers in October, November and December of up to 8%, but there had been a significant increase in recent days of patients who are sick with flu and respiratory illnesses.
Hospitals impose visiting restrictions over flu outbreak
Two hospitals have put visiting restrictions in place following a number of cases of flu.
University Hospital Limerick said it had seven confirmed cases with a number of other patients symptomatic.
As a result, the hospital is restricting visitors to one person per patient only and said visiting hours must be strictly adhered to.
It also said that children should not be brought on visits anywhere in the hospital.
The number of confirmed flu cases at Cork's Mercy University Hospital is 11.
MUH Clinical Director Dr Kieran O'Connor said: "In this context, visiting is being restricted to the hospital in the interest of patient safety.
"The hospital is seeking the public's cooperation with the restrictions, but will deal with exceptional cases on an individual basis".
He said that people with flu-like symptoms should visit or phone their GPs rather than go to the hospital's Emergency Department.
The Health Service Executive has urged people to get the flu vaccination and said the number of reported cases of flu had increased in the week before Christmas and it "is now actively circulating in Ireland".