The Ombudsman for Children is to investigate the official handling of the HSE's audit of child protection in Catholic dioceses outside Dublin, the results of which were published on Wednesday.
Emily Logan announced that she will examine whether the safety of children or good public administration were compromised by the HSE's and the Department of Health's acceptance of the church's refusal to answer section five of the audit.
Section five sought detailed information on complaints and allegations of clerical child sexual abuse, asking whether these had been notified to the civil authorities.
The bishops said they could not respond until legislation envisaged in 2005 by the Ferns Report was introduced.
The HSE says that in consultation with the Department of Health, and after sharing independent legal advice with it, the controversial section was dropped from the audit.
A spokesperson for the Ombudsman emphasised that she has no jurisdiction over the Catholic Church, but was duty-bound to investigate the State's handling of the issue.