The HSE was told "we can't continue like this" in discussions over enormous overruns in their annual spending.
Department of Health Secretary General Robert Watt told HSE CEO Bernard Gloster that more needed to be done to get expenditure under control.
The discussions came in April after officials said between €1.5 and €2 billion more than expected would be needed to balance the books for 2024.
In an email, Robert Watt wrote: "I am trying to understand this. What increase in the first quarter have we profiled and what is the actual increase? And what are we going to do to get back on track?"
Mr Watt was told that there had been an almost 15% increase in spending in the first quarter of this year compared to 2023.
"Is this just acutes [services]?" he asked officials.
A colleague replied: "These percentages relate to total current spending. Not just acute services."
Mr Watt answered, saying: "I was told other areas are okay. Are they out of control too?"
In response, a senior official said that while acute services were the "primary problem", other areas were also running over budget.
Asked for further detail on the cost overruns, the HSE CEO Bernard Gloster said the situation would have been worse if not for a pause on recruitment in the health sector.
Mr Gloster said: "I have repeatedly pointed out the risks on this and while it is a shared one between us, I can’t do anything further with it at this point."
In response, Mr Watt said: "Bernard, we need to do something more here. We can’t continue like this."
In a follow-up email to Health Minister Stephen Donnelly that month, Robert Watt warned that the overrun for the year could end up being around €1.5 billion.
He wrote: "I am very concerned about these trends … we have issued instructions regarding non-pay and hopefully this will lead to an expenditure slowdown."
Mr Donnelly responded saying: "Those trends are indeed very concerning. I will alert party leaders."
However, Mr Donnelly said there was likely to be a delay in getting a decision on what to do because of the changeover of Taoiseach.
"The change has, very understandably, delayed getting a political decision," the minister wrote.
"The new Taoiseach’s team are aware of the urgency."
There were also discussions that month over the continued use of private beds with between 140 and 160 being sourced from the private sector each day.
The HSE chief Bernard Gloster had told the department they were helping manage challenges around hospital capacity.
However, Mr Watt told Minister Donnelly they were not funded and continuing it throughout the year would lead to a large bill.
Mr Donnelly responded saying: "We need to do the best by patients. Can I have your view please on the best way to proceed.
"In other emails in May, Robert Watt also flagged concerns over what he said were ongoing problems at University Hospital Limerick (UHL).
He had been told that on a specific weekend in May, only one emergency consultant would be in UHL on Saturday and Sunday from 8am to 1pm, and afterwards available on call.
An email to Bernard Gloster and a senior colleague said: "I would like to have a conversation about this please.
"Notwithstanding the many patient safety issues experienced in Limerick, and the ongoing trolley issues … the rostering of senior decision makers at the weekend is unacceptably low."
A spokesman for the HSE said the discussions had taken place ahead of a two-year agreement on funding that was announced during the summer.
He said: "During the past year we have updated and improved spending controls so as to ensure we get the best value from the resources we have."
"We agreed a pay and numbers strategy with the government … [and] additional mechanisms to manage non-pay costs were introduced in July and we are working daily to manage and reduce costs without reducing front line services."
