Rev Victor Neill’s comments came after police officers stormed a service at Ballynahinch Congregational Church after a minister was surrounded by a group of angry worshippers on Sunday.
During the extraordinary standoff, the Rev George Speers used a megaphone in a bid to drown out those jeering him from the pews while preaching.
Years of tensions and disputes have split parishioners into church-goers who support the minister and those who want the minister to leave.
“We wouldn’t wish this on anyone, we haven’t seen anything like it before,” said Rev Neill, the chairman of the Congregational Union of Ireland.
“There are sometimes issues like this – but I have never seen them reach this stage.”
Ballynahinch Congregational Church is one of the 27 that makes up the Congregational Union of Ireland.
But the governing body cannot intervene unless it is invited.
Rev Neill said: “We can do no more than offer our help and wait and see. We issued our statement to both sides but no-one has come forward.”
Geoff Buchanan is the leader of the Boys’ Brigade at the church and told the Belfast Telegraph he understands both sides in the bitter row.
But he added that he didn’t think the behaviour of those protesting was appropriate in a church setting.
“There were a lot of young children there and it is hard to justify that sort of behaviour and level of noise,” he said.
“I am pretty neutral in this, but both sides have dug trenches and are very reluctant to back down.
“There needs to be a cooling off period and mediation so both sides can learn to be in the same building together.”
The long-running dispute which reached boiling point at the weekend has had a huge impact on those involved.
Trustee Trevor Carruthers (69) said: “I was 12 stone 6 when this all began and I dropped to 10 stone 6.”
They roared “Out, Out, Out”, clapping, whistling and cheering, surrounding the pulpit.
One man was spoken to by police for unplugging the organ.