Ombudsman for Children Emily Logan has suspended her investigation into the HSE's handling of the Child Protection Audit of Catholic Church dioceses.
Ms Logan has accused the Health Service Executive of failing to co-operate, despite public and private assurances that it would.
The HSE has said it will contact the Ombudsman today to try to resolve the row.
The HSE says it has been fully co-operating and will continue to do so. It says it is disappointed that the Ombudsman has chosen to suspend her investigation.
Speaking on RTÉ's Morning Ireland, the HSE's assistant national director of primary community and continuing care, Hugh Kane, said he had not spoken to the Ombudsman about the issue because he did not know of her outstanding concerns.
The Ombudsman wants to find out if any child was adversely affected by how the HSE's audit was carried out and managed.
She wrote to the Department of Health and HSE on 9 January, requesting that all relevant documentation be provided to her office within 21 days.
Ms Logan says while the department has engaged with the investigation, the HSE has failed to provide any of the documentation requested.
This includes correspondence between the HSE and Catholic Church, after a section of the audit questionnaire requesting detailed information on complaints and allegations was not completed.
The bishops said it presented legal difficulties in relation to confidentiality. Ms Logan is investigating if the HSE properly pursued that information.
Ms Logan says the HSE initially sought and was granted more time to respond to her office, before later asking her office to appoint a senior counsel to discuss the investigation with its senior counsel.
But the Ombudsman argues her office already has the power to compel documents to be produced.
