Fiona Brown, principal of Desertmartin Primary, also said the Church of Ireland was “disrespectful” over plans to close the school.
It was to merge with nearby Knocknagin Primary to become Northern Ireland’s first joint-faith school.
But the four main churches have not been able to reach agreement over the ethos of the new school.
That has meant Desertmartin – which is more than 130 years old – is now set to close as its enrolment has fallen to only 11 pupils.
Ms Brown admitted that the school was unsustainable, but said that since the joint-faith school plans were announced in 2016 staff, parents and pupils had been kept in the dark.
“The idea was that the churches would come together,” she said.
“Knocknagin is a Catholic maintained school and we are a Church of Ireland maintained school.
“We would have a school with a Christian ethos where both faiths would be represented, but no faith as well, where there wouldn’t be the segregation that there has traditionally been,” she said.
“Desertmartin has traditionally, geographically, been a very divided community with no neutral meeting space so until the schools were working together, people had very limited chances to meet their neighbours if they came from a different background.”
Pupils and staff in both schools, which are about half a mile apart, have been working together through shared education classes for a number of years, which led to the merger proposal.
“We trusted the churches to get on with it and we understood they were getting on with it,” Ms Brown said.
“Nobody will tell us what the difficulties are either, what’s delayed the process so long, and that’s very frustrating and actually very hurtful for us at this point.
“I find that difficult because I am a member of the Church of Ireland and I find it very hurtful at a personal level as well as a professional level from the point of view of our parents and pupils that anyone would be so evasive.
“It makes me very uncomfortable, it’s very disrespectful I think.
“We feel very let down.”
In November, the Education Authority said that Desertmartin Primary School would close in August 2020, or as soon a possible thereafter.
In a statement the Derry Diocesan Board of Education of the Church of Ireland said the interests of the pupils at the school had been “paramount” throughout the process.
“The board has consulted governors, staff, parents and guardians – via the Education Authority – and engaged directly with staff and governors,” it added.
“It would be inappropriate for the board to comment further while the [education] minister considers the school’s future.
“But the board will continue to offer its support to staff, governors, parents, guardians and children whatever decision the minister takes.”