Archbishop of Glasgow Philip Tartaglia has written to Michael Russell, the Education Secretary, asking for the decision to be called in for scrutiny.
The move comes after councillors from East Dunbartonshire backed plans to close St Joseph's Primary in Milngavie, on the outskirts of Glasgow.
Under the proposal, pupils will go to a new school in neighbouring Bearsden following a merger with St Andrew's Primary.
The council acted against a backdrop of falling school rolls and funding cuts, with East Dunbartonshire seeking to make £20 million savings over the next three years.
However, parents and the Church say rolls have increased in recent years and argue the move will leave Milngavie with no Catholic primary school.
Archbishop Tartaglia has now written to Mr Russell to ask for the decision to be called in under education legislation.
In his letter to Mr Russell, Archbishop Tartaglia said: "I greatly regret to say that, despite our best efforts, the council has proceeded with a decision which I believe to be manifestly unjust and discriminatory against Catholic children and parents in this community.
"While the council appears content to provide three non-denominational schools in the town of Milngavie and one in Baldernock, there will be no Catholic school provision if this decision stands.
"The removal of the only Catholic school ... could not be more significant for this community."
Archbishop Tartaglia said the council's argument that larger schools were necessary to ensure the provision of efficient services was flawed.
Laureen McIntyre, chairwoman of the St Joseph's parent council, welcomed his intervention. She said: "We are delighted that Archbishop Tartaglia has written to the Scottish Government asking them to stop the closure of St Joseph's. Ministers must consider the Church's views very seriously when making their decision."
However, Gordon Currie, director of education for East Dunbartonshire, said St Joseph's roll had dropped by 23 per cent in the last decade. "This proposal, to provide one modern, well-equipped school to replace two very under-occupied schools ... represents a significant investment in Catholic education of almost £9m," he said.
"Far from discriminating against Catholic education, this council ... remains committed to providing high quality denominational education."
He said an Equality Impact Assessment of the proposals proved there was no intention to discriminate against a particular group.