The Charity Commission for Northern Ireland has begun an inquiry into the Presbyterian Church in Ireland (PCI) following the resignation of its moderator last month over "serious and significant failings" in safeguarding.
The commission has the power to launch the investigation because the church is a registered charity.
In a statement, it said that it will work with the church to ensure that "safeguarding and governance issues are addressed and appropriate remedial steps put in place".
PCI's Acting Clerk Rev Dr David Allen said the church welcomed the announcement and has been working with the Charity Commission over the last number of weeks.
"PCI is fully committed to working with the Charity Commission to facilitate this inquiry and will cooperate fully in all aspects," he said.
Dr Allen said the church has committed itself to "doing whatever is required to regain the trust that we have lost".
He said a number of resolutions will be proposed at the Special General Assembly this Thursday which the church believes "will begin to make the changes required".
The PSNI announced last month that it was launching a criminal investigation into safeguarding concerns.
The charity commission's decision to lanch a statutory inquiry into the church "and all its component elements" was made in a statement.
"Safeguarding is fundamental to maintaining public trust in charities," its Chief Executive Frances McCandless said.
"Every charity must make the safety and wellbeing of those they serve their highest priority."
A report drawn up in the wake of the safeguarding failings said the Presbyterian Church in Ireland was in a "shameful" position.
A senior church committee has recommended a review of "governance, culture and integrity issues" as well as safeguarding.
The report and its proposals will be debated by ministers and elders at a special meeting of the decision-making General Assembly in Belfast on Thursday.
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The PSNI said it is aware of the announcement by the charity commission.
In a statement, Assistant Chief Constable Davy Beck said the police investigation remains active and "will not be affected by the Charity Commission's inquiry processes".
