Officials will begin to cross-reference the names of all accused and complainants with gardai files to ensure that dioceses are following through on their commitment to report all allegations of child sexual abuse to the civil authorities.
A December deadline was originally set for dioceses to submit their audit returns.
However, this was pushed back to January after the HSE said it would be seeking more detailed information than first indicated.
An HSE spokesperson said that although this second deadline had passed with only half of dioceses supplying the information requested, all audit returns had now been received.
"On January 15, a week after the deadline given by the HSE in December, 12 of the 24 dioceses had either not responded at all or had advised the HSE that they would be delayed in responding," she added.
"After follow-up with these dioceses by the HSE, the last of the information requested was received by the end of February and the HSE can now confirm that it has received all diocesan audit returns."
While a small number of dioceses have yet to supply their child protection policies, the HSE said this would not hinder it in completing the report.
The finished report will be handed over to Children's Minister Barry Andrews, who may then ask that the state inquiry be extended into more dioceses.
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