The Holy Trinity National School in Westport held a protest on a site they say was promised to them for a new building, but instead it is being allocated to another school in the town.
The site is being allocated to the Sacred Heart all girls secondary school, which the department says is in urgent need of temporary accommodation.
As a result, over 150 people turned out to protest at what they say is the "gross injustice" of seeing their 14-year fight for a new school for Holy Trinity being taken away from them out of the blue.
They said that they were told another school needed that site urgently, and the plan is for the Sacred Heart secondary school to move into the vacant site next September.
Orla Brickenden, principal of the Holy Trinity National School, said that people were angry, frustrated and disappointed.
"Our small little Church of Ireland school in the heart of Westport was on the road to getting our new school building," she said.
"We just don't think it's fair that the Department of Education, the building section and the Minister for Education have done this to us, and we just think it's just so very unfair."
Ms Brickenden said that their school should not be the solution for another school's problems.
"We all know that the Sacred Heart has building problems and building issues, but we firmly believe that we are not the solution to the Sacred Heart building problems, and we can't be the collateral damage for them temporarily taking over our building.
"And what does that mean? There's no timeline. It could be decades.
"So while we understand where they're coming from, we're not the solution."
The Sacred Heart secondary school has over 500 pupils and the Department of Education cited an "urgent need" to find temporary accommodation on health and safety grounds.
The three-teacher 19th century Holy Trinity school is also deemed "not fit for purpose" but its needs are seen as less urgent.
In previous correspondence, the Department of Education acknowledged the concerns of the Holy Trinity School.
"The Department is aware that the use of the former Scoil Phádraig building as an interim solution for Sacred Heart School has raised some concerns on the part of the Holy Trinity NS community," it said.
"In that context, the Department has had very productive engagement with the school's patron, the Bishop of Tuam, Limerick and Killaloe.
"Department officials have confirmed to the patron that there is a continued commitment to the delivery of the Holy Trinity NS project and set out some assurances and proposals of how the Department can support Holy Trinity NS in the interim as well as enhancing the overall outcome for the school in the medium-term."
Eoin Holmes, a member of the Holy Trinity board of management, said that both schools do get on well but that the decision needs to be reconsidered.
The Sacred Heart school declined any interviews but said that it acknowledges the concerns and frustrations of the Holy Trinity school.
In a statement, it said that it is confident that the school's relocation will be for a "very short duration".
The protesters marched to the derelict Scoil Phádraig site which was first offered to Holy Trinity by the Sisters of Mercy but will now see the Sacred Heart School planning to be in place by September 2025.
The timeline remains unclear for both schools as to when they will see their new builds.
Sr Kathleen Friel, a Sister of Mercy, took part in the protest and said: "This particular scenario has developed in a very unacceptable manner, and I believe firmly that that is because the local people were not consulted.
"We forget that there's a lot of wisdom and information amongst local people when it comes to issues of this nature. So that is really why I stand here, and I'm very upset at the lack of consultation.
"The information I have is in the public domain.
"And I listened to the school principal of Holy Trinity yesterday, who clarified the situation very well and I certainly did not gather from that, that there was any level of consultation that may have furthered this cause, without the divisiveness and the negativity that is now present."