The church made the admission in a report that recommended the continued use of the deals.
It cited theological arguments as justification for its position, including that on “numerous occasions Jesus specifically imposed confidentiality requirements on individuals and groups, including his own disciples”.
The report also said NDAs should not be used to cover up wrongdoing.
Over the past year, this newspaper has revealed the identities of four of those who signed agreements. The others are unknown.
Trainee Presbyterian minister Tom Finnegan and his wife Renée, a former PCI communications assistant, signed NDAs as part of their settlements.
They previously said they were not made fully aware of the consequences and did not truly offer informed consent.
Requests from the couple and Rev Professor Laurence Kirkpatrick, who was also subject to an NDA, to be released from the agreements were rejected last November.
Mr Finnegan told Sunday Life: “The use of scripture to support NDAs, and implying that Jesus would use them, is a twisted view. The report is blasphemous. It’s sickening to read. It shows they have learned nothing and are out of step with legislation changes. It’s now unlawful to use NDAs in England in cases of harassment and discrimination, and it’s the same in the Republic of Ireland. New legislation needs to be implemented here too.”
Mr Finnegan also hit out at a church argument that Christians shouldn’t take other Christians to court, saying that NDAs were “permanent legal threats to silence people”.
The report was written by a taskforce set up to investigate the use of NDAs. Among its members are acting clerk Rev Dr David Allen and head of HR Sarah Leung, both named respondents in Mrs Finnegan’s case of alleged unfair dismissal due to race and sex discrimination.
Ken Swarbrick also sits on the panel. He represented the church at a tribunal last December where a judge accepted arguments made on behalf of this newspaper to allow publication of some of the details of Mrs Finnegan’s case, which was settled without an admission of liability.
In its 11-page analysis, the taskforce recommended “a balanced approach” in using confidential agreements, saying that in the past five years, nine NDAs had been used but 650 people had left the PCI’s employment.
It claimed the agreements protected the church and employed individuals from malicious comments.
However, Professor Kirkpatrick said that neither he nor the others were consulted about the effect of NDAs, and called on the church to ban them.
He added: “They (people who signed NDAs) have found the experience traumatising, unfairly levied by this large employer organisation, and foisted upon them in the face of personally prohibitive financial costs to maintain wider public ignorance of alleged workplace misconduct and improper employment practices.
“These four individuals would like to speak about their experiences, but the PCI insists on enforcing NDAs and are therefore feeding the suspicion that they are hiding something. Surely the church has nothing to fear if they are innocent in these matters.”
Former PCI head of safeguarding Dr Jacqui Montgomery-Devlin also said she felt under pressure to sign an agreement after a dispute with the church.
The church said the General Assembly would take resolutions outlined in the report prayerfully, adding that it would be “inappropriate to comment on any aspect of the business” before next month’s meeting.