Members agreed at a Special General Assembly in Belfast that a full independent external review of safeguarding would be conducted within the denomination.
The Church's Moderator, Rev Richard Murray, apologised to those who had been hurt or harmed as a result of the church’s safeguarding failings, saying to those it let down, "we are deeply ashamed and sorry".
Convener PCI’s General Council Rev Dr David Bruce said the starting point was and remained "a profound concern" for those who had been harmed, or impacted by institutional failings.
"We have described this as 'shameful' because it is," he said. He added that there would be no cover up.
Members agreed that the new department would have external oversight through a Safeguarding Supervision Panel.
The department will be funded from congregations and "at an appropriate time", a full, independent, external review of PCI Safeguarding at all levels be conducted.
It was described as an attempt to redefine "the place and importance" of Safeguarding in the PCI.