The former speaker of the Assembly resigned as an elder from the church in June 2018, saying he was concerned about a new forthright expression of its stance against same sex relationships.
An elder of 30 years standing, he also disagreed with it loosening ties with the Church of Scotland - after it moved to approve same sex relationships - and its decision to leave the World Council of Churches.
After his resignation he worked together with former Presbyterian minister Roy Simpson to compile a dossier of allegations against the church containing interviews with 12 people.
He noted that despite submitting the 150-page report to the commission three years ago it has yet to question the church about the matter.
He therefore called into question whether the commission is "actually fit for purpose".
"Is it actually there doing what it's supposed to do? Three years on I have to say one has to be questioning that," he told the BBC.
He also challenged the church's use of non-disclosure agreements (NDAs) - legally binding documents that protect confidential information between two parties and prevent staff and ex-staff speaking publicly on specified issues.
"If ministers for example do open up and try to speak about things, they're accused of contumacy, they're accused of bringing the church into disrepute," he said.
In a number of cases which made headlines in recent years, the church has argued that disciplinary action against certain clergy or elders was justified because it considered that they had publicly countered official church teaching on marriage and same sex relationships.
The co-author of the dossier, Roy Simpson, claimed the report was "only really the tip of the iceberg".
"These people are very decent people, they're upright people, they're people who have given their lives in service to the church, they're not cranks and they don't tell lies," he said.
"They feel like they've been subject to spying, stalking, they've been subject to bullying, they've been subject to harassment and all sorts of derogatory comments said about them."
The Charity Commission responded that the case is "complex" and is therefore taking longer than usual to complete.
"The Presbyterian Church in Ireland case involves a lot of detailed and sometimes quite complex information, which has resulted in the investigation taking longer than usual to complete,” it said.
"While we aim to deal with all cases as quickly as possible, factors such as how complex a case is, any potential risk to the charity’s assets or beneficiaries, whether other regulators or statutory bodies are involved and available resources all affect how long an investigation may take," it said. "Some cases may also require ongoing monitoring.”
It hopes to move towards "a suitable outcome" over the next few months, it added.
The church responded that the commission only informed it about the dossier in June this year – prompted by a media inquiry - but has not yet asked it for any comment about the allegations.
"Should we be approached by the Commission to do so, we will cooperate fully," it added.
Lord Alderdice was invited to comment.