The opening of the inquiry – the commission’s highest level of investigation – follows the Church’s recent announcement regarding safeguarding failings.
In a statement the Commission said the move reflects “the serious nature of the concerns raised” and said they will work with the church to ensure the safeguarding and governance issues are addressed and “appropriate remedial steps put in place”.
It comes after former moderator Rev Trevor Gribben stood down after a review found “serious and significant failings” in central safeguarding functions from the period 2009 to 2022.
It emerged that failures included situations where the church did not respond when people who had suffered harm sought help and instances where offenders returned to worship in church but were “inadequately monitored”.

The headquarters of the Presbyterian Church in Ireland
Head of Presbyterian Church in Ireland to step down over safeguarding failures
The Police Service of Northern Ireland (PSNI) subsequently launched a criminal investigation into the matter which remains active.
The PCI welcomed the police probe and said it would be co-operating fully.
Frances McCandless, chief executive of the Commission, said: “Safeguarding is fundamental to maintaining public trust in charities.
“Every charity must make the safety and wellbeing of those they serve their highest priority.”
In a statement, the Police Service of Northern Ireland confirmed its ongoing investigation into safeguarding concerns connected to the Presbyterian Church in Ireland remains active.
Assistant Chief Constable Davy Beck said the PSNI is working closely with the Charity Commission.
“As previously confirmed, the Police Service has an ongoing investigation into safeguarding concerns connected to the Presbyterian Church in Ireland,” he added.
“This work remains active and will not be affected by the Charity Commission’s Inquiry processes.
“Safeguarding is a priority for the Police Service. We take any information suggesting risk or potential criminality extremely seriously.
“We are working closely with the Charity Commission and with other statutory and community safeguarding partners.
“This coordinated approach ensures that any concerns raised are fully examined and that appropriate steps are taken to address any criminality and to protect those who have been harmed and need help and support to access a wide range of services.”

Former Presbyterian moderator Rev Trevor Gribben who stood down after a review found ‘serious failings’ in safeguarding (Liam McBurney/PA)
Assistant Chief Constable Beck urged anyone affected or with information that may assist the police to come forward.
He added: “Dedicated specialist officers are available to ensure victims can access the criminal justice system and provide advice and support where necessary.
“Anyone with concerns can contact our dedicated team via email: PCIenquiry@psni.police.uk or by phoning 101.”
The PCI has around 180,000 members belonging to more than 500 congregations across 19 regional presbyteries across the island.
The church is set to hold a special General Assembly later this week.
A large gathering is expected at Assembly Buildings as ministers and elders meet in the wake of the church crisis.
The special assembly will be live streamed and be open to members of the public and the media.
The PSNI have advised that if victims want to avail of support, or want to talk to someone who can help them navigate what is a triggering or traumatic time, they can contact Victim Support NI helpline on: 028 9013 0405.