The body representing Catholic schools has accused the Northern Ireland Office (NIO) of excluding it from an event on Northern Ireland's future.
The NIO is behind a conference called A More Confident and Inclusive Northern Ireland.
In a speech at it, Northern Ireland Secretary Brandon Lewis said the UK government was set to do more to promote integrated education.
The umbrella body for controlled schools also said it was not invited.
The Council for Catholic Maintained Schools (CCMS) and Controlled Schools Support Council (CSSC) described their absence as "concerning" and "alarming".
A spokesperson for the UK government said the conference brought together a variety of different voices and that it would continue to engage "across all sections of society going forward", including with CCMS and CSSC.
The three-day conference began on Wednesday and was set up by the NIO and government agency Wilton Park.
Mr Lewis told the event that a new government programme would promote the benefits of integrated education to parents, teachers and pupils.
But the chairman of the CCMS, the Bishop of Derry, the Right Reverend Donal McKeown, and its chief executive, Gerry Campbell, have written to Mr Lewis criticising their exclusion from the event.
In their letter, seen by BBC News NI, they said the absence of CCMS was alarming.
"The programme asks, 'what can be done to ensure the views of all young people, from all communities, are given the opportunity and tools to engage?'," their letter said.
"Given that the broad family of Catholic schools represents one of the largest providers of education in Northern Ireland, the notable absence of participation and involvement with the Catholic sector is alarming.
"Indeed, it is rather ironic that a conference with a focus on building inclusion is actually exclusionary in its approach."
Bishop McKeown and Mr Campbell said CCMS strongly supported efforts to promote peace, reconciliation and understanding in Northern Ireland.
"The conference programme asks the question: 'How to work together to build a confident and inclusive Northern Ireland for all?' their letter continued.
"Coupled with the exclusion of all Catholic schools and the bodies who represent them at the landmark event despite the track record of excellence and success within Catholic education, we ask the question to the Northern Ireland Office: 'Does the NIO recognise the contribution of Catholic schools to supporting our young people to reach their full potential and where does the NIO see Catholic schools within its future vision?'"
About 150,000 pupils go to around 450 Catholic maintained schools in Northern Ireland.
Controlled schools are those formerly managed mainly by the Protestant churches, which were transferred to the state in the 20th century.
There are about 450 controlled primaries and post-primaries and many have pupils from a range of backgrounds.
The umbrella body for those schools - CSSC - also said it was not invited to the NIO conference.
In a letter to principals of controlled schools, the chief executive of CSSC, Mark Baker, said it was committed to children and young people being educated together.
"We have expressed our concern that the voice of the controlled sector has not been included at this event," he wrote.
"We raised our concerns that any conference which includes a discussion on the future of education would be held without the voice of 49% of the schools in Northern Ireland being present.
"We were given assurances that the NIO wish to engage with the sector."
The two bodies had previously expressed concern about the impact of a new law requiring the Department of Education (DE) to give more "support" to integrated education.
A UK government spokesperson said: "The Wilton Park conference has brought together a variety of academic, public policy, and third sector voices to consider how to work together to achieve a more confident and inclusive Northern Ireland.
"A broad range of factors are under consideration, including skills, education, the economy and social integration.
"The NIO will continue to engage across all sections of society in its work going forward, including the Council for Catholic Maintained Schools and the Controlled Schools Support Council, and bodies in the education sector."