The hospital which had its NTPF funding suspended in mid April is Beaumont Hospital in Dublin, a major public facility.
It is understood the issue is very different to what was found at CHI in an internal review and it does not relate to a consultant-led issue.
The Department of Health was first alerted to the issue at Beaumont on 11 April and the Minister for Health was advised on 14 April.
Beaumont Hospital has said that in March this year, it approached the NTPF of its own volition for the purpose of securing necessary clarifications in relation to activity conducted under the terms and conditions of an existing Memorandum of Understanding.
Beaumont Hospital said it can confirm the decision of the NTPF to discontinue funding of patient activity from 11 April.
"As a consequence, the hospital engaged directly with the HSE for the purpose of seeking an independent review of related issues.
"The process is ongoing and the Hospital will continue to co-operate fully with the review in all respects. The hospital has maintained access with minimal impact on patient care," the hospital added.
The identification of the hospital comes after the National Treatment Purchase Fund (NTPF) confirmed it suspended waiting list funding at a second hospital over "potential financial irregularities".
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The NTPF said it alerted the Department of Health and HSE about the irregularities in relation to NTPF-funded insourcing work at the public hospital.
All insourcing work with that hospital has been suspended since 11 April.
In a statement Minister for Health Jennifer Carroll MacNeill said that in April, the NTPF alerted the Department of Health and HSE about potential financial irregularities in relation to NTPF-funded insourcing work at a public hospital.
"It has suspended all insourcing work with that hospital pending examination. The matter has been referred to the HSE's Internal Audit team.
"The Minister is awaiting the outcome of the wider review of all insourcing initiatives across the system which she asked the HSE CEO to undertake," the statement added.
The NTPF said it immediately informed the Department and HSE of these concerns and is working with them in relation to the ongoing review.
"The matter has been referred to the HSE's Internal Audit team. The NTPF is restricted from making further comment at this stage," it added.
In a statement, the HSE said that it understands that a Section 38 Hospital received an allegation associated with a single NTPF-funded clinic it said that the NTPF notified the Department of Health that it had received this information.
The HSE added that the Department of Health on the same evening, notified the relevant HSE Regional Executive Officer, who in turn immediately notified the CEO.
"Almost immediately, in consultation with the CEO of the HSE, they commissioned an internal audit to establish the facts. The NTPF are aware of this.
"All information gathered during this process relevant to the NTPF will be provided to the NTPF. This remains an allegation. We take it very seriously, but the information in relation to it needs to be gathered and the facts have yet to be established," the statement concluded.
It comes as the NTPF said that following a meeting of its Board, it is to resume insourcing work, effective immediately, with Children's Health Ireland (CHI).
It follows a review of the assurances given by CHI in relation to its ongoing compliance with existing NTPF protocols and procedures.
Funding was suspended recently after the NTPF learned of details of an unpublished CHI internal report into practices in one of its hospitals.
Today the Board and Executive of the NTPF said it remain deeply concerned that there was a breach of its processes by another public body.
The NTPF said it will now increase governance and oversight across its insourcing work with public hospitals, who up to now have been responsible for this internal governance.
The NTPF has notified the Department of Health and HSE of this decision.
The NTPF has written to all public hospitals with whom it funds insourcing work to obtain further confirmation that all work is carried out in line with the NTPF's processes and procedures in this regard.
A strict deadline of next Monday, 16 June has been given for the completion of these replies and the NTPF will report on this to the Department and the HSE separately.
