The row is over the refusal by the province's Department of Education to set up new bodies for the Protestant churches, who fear their influence over education is being further reduced.
Church leaders have launched furious attacks on senior civil servants in the Department, and the issue featured at the Church of Ireland, Presbyterian and Methodist conferences over the last few weeks. All three demanded an immediate moratorium on controversial plans to axe one of the province's five education area boards which would also cut the links between education authorities and church representatives on governing bodies.
The Church of Ireland demanded the immediate intervention of both the Northern Ireland Select Committee and the Public Accounts Committee to avoid an education crisis. The Church of Ireland also accused senior Department officials of "cynical insensitivity" to local opinion, and urged an inquiry into why the present department team has "little if any credibility among their education partners".
They and the Presbyterian church said Northern Ireland Minister Michael Ancram, currently involved in delicate political talks over the peace process, should consider if he has time for education.
The Methodist Board of Education said it was deeply concerned an injustice was being perpetrated against the Protestant community with continued failure to give parity. The churches are angry that special councils have been set up for the Catholic maintained sector and the integrated schools lobby, while their role has gradually been eroded.
But Church of Ireland primate Dr Robin Eames denied the demand for Protestant councils in each area board was sectarian or competitive.
"It is not our intention to say that because the Roman Catholic church has got its body we must have one. We welcome this for the Roman Catholic church, but it would ease the problem for the non-Catholic churches if there was a similar body for us."
The Church of Ireland education spokesman, the Reverend Houston McKelvy, said: "There is an increasing lack of confidence by many involved in the daily delivery and management of education in those heading the Department at present."
Presbyterian education spokesman the Reverend Derek Poots said that if Mr Ancram was too busy with political talks, consideration should be given to changing his portfolio.
Methodist minister the Reverend Wesley Blair said the creation of the Council for Catholic Maintained Schools had been one of the most retrograde steps in education in Ulster in the past 50 years.
The Department has refused to make any comment until Mr Ancram makes final decisions on the future shape of administration of education in the province.