The archdiocese of Glasgow expressed concern over proposals to shut St Joseph's Primary in Milngavie, near Glasgow.
The school, which would merge with St Andrew's Primary in Bearsden, is the only Catholic primary in the immediate vicinity.
A spokesman for the archdiocese said: "We responded to the consultation from East Dunbartonshire Council to express preference for the retention of St Joseph's Primary in Milngavie and St Andrew's Primary in Bearsden.
"Both are excellent schools which are well supported by the local Catholic community.
"The archdiocese has grave concerns about this proposal which would remove the Catholic educational presence in Milngavie, and those concerns are shared by the local Catholic community."
According to the results of a council consultation, a majority of people from Milngavie also oppose the proposal – with only 17% agreeing with it.
Laureen McIntyre, chairwoman of St Joseph's parent council, said: "The parents are asking whether it is simply that it is a small school and an easy target or is it because it is a Catholic school? The closure of St Joseph's Primary would result in the removal of any denominational provision for the area of Milngavie.
"In fact, there would only be one denominational school left on this side of the authority.
"Councils have a duty to provide sufficient denominational educational provision for an area. Can councils now define an area in any way to suit their own agenda without a care for the population served?"
Andrew McFadyen, a parent at St Joseph's Primary, added: "Families in Milngavie should not be forced choose between their faith and community. Our children have the same right as any others to be educated in Milngavie."
Gerry Cornes, chief executive of East Dunbartonshire Council, said: "No decisions will be taken until the council meets on 27 March."