Rev Dr Richard Kerr was commenting on the arrests, first reported by the BBC, of individuals in connection to the PSNI’s investigation of safeguarding concerns in the Presbyterian church.
He also paid tribute to the “bravery and strength” of people who have come forward with complaints about safeguarding issues in the church.
The police have received more than 100 referrals as part of their investigation into the PCI.
Reacting to news that two people had been arrested, Rev Dr Kerr said: “We remain saddened by the circumstances which gave rise to the PSNI investigation and are continuing to assist the police in every way we can.
“We also recognise the bravery and strength of those who have already come forward and continue to encourage all victims, survivors and those with concerns to do so.
“We have been made aware by PSNI that a number of arrests have taken place as part of their ongoing investigation but we cannot make any further comments in this regard.
“Alongside the investigation, we are continuing to improve the safeguarding capabilities across the denomination.
“We have created a stand-alone safeguarding department, staffed with new safeguarding officers, a policy specialist and a dedicated training officer.
“In May and June this year we trained or retrained approximately 2,800 leaders and volunteers, and we have a significant training programme in place for the next few months with over 40 training events being organised.
“Additionally, we have revised and reissued our safeguarding policies and procedures, which are now in force throughout the denomination both north and south.
“We recognise that this continues to be a difficult time for many who placed their trust in the Presbyterian Church and we remain mindful of any who have been hurt by our actions or inactions.
“We are committed to delivering the progress and change that is required to put things right.”
A PSNI spokesperson said, “The Police Service of Northern Ireland’s investigation into safeguarding concerns relating to the Presbyterian Church in Ireland continues.
“To date, 127 contacts have been made with police from potential victims and/or witnesses.
“Two people have been arrested as part of the investigation. Enquiries remain ongoing.
“Police continue to work closely with partner agencies to ensure a safeguarding-led approach throughout the investigation.
“The PSNI continues to encourage anyone who has information or concerns to contact them directly or reach out for support via Victim Support NI.