The government has "called in" proposals to shut St Joseph's Primary in Milngavie near Glasgow.
The council plans to build a new denominational primary in nearby Bearsden - replacing both St Joseph's and the school on the site at present.
Parents at St Joseph's and the Catholic Church have been fighting the plan.
East Dunbartonshire Council plans to merge St Joseph's Primary with St Andrew's Primary in neighbouring Bearsden.
The merged school would be sited in a new building on the current St Andrew's Primary School site.
When the Scottish government calls in any proposal to close a school, it examines the process followed by the council and the information used to reach the decision.
But it cannot simply overturn a decision because it disagrees with it.
A letter informing the council of the government's decision said ministers were concerned by allegations the council's consultation document contained inaccurate information.
It also said concerns raised by Education Scotland may not have been fully addressed by the council in the consultation.
A spokesman for the parents at St Joseph's said: "Parents are delighted that the Scottish government has decided to call this process in.
"It is now clear that the way East Dunbartonshire Council has conducted this process has more holes than a colander.
"We believe and ministers appear to agree that our children will receive the best possible education in their own community."
Council leader Rhonda Gheekie said: "This is a complex process and it's understandable that the Scottish government wants to investigate the proposal further.
"We welcome the same opportunity to explain in greater detail the educational benefits that we believe will come from our proposal to build a new £9m denominational primary school for Bearsden and Milngavie.
"We understand the significance of any new school build for the local community and what we all have in common is that we want to get it right to ensure the best possible future education for the young people in the area."
The council said its proposals were part of its Primary School Improvement Programme to modernise the primary school estate. This aims to deliver state of the art primary schools which are better for pupils and cheaper to run and maintain.
Ms Geekie added: "The council must save a further £20m from its budget over the next three years. On top of the £40m we have already saved, doing nothing in terms of our school estate to help address this was never an option.
"We have to ensure that our school buildings are as cost-effective as they can possibly be to ensure that we are getting value for money from our budget spending."
Meanwhile, the council's plan to close two primary schools in Kirkintilloch and establish a new £7m school to replace them are to go ahead.
The new school there is expected to open in 2016 or 2017.

A man, aged 28, and a woman, aged 35, have been arrested on suspicion of the possession of firearms over the incident at Chapel Street.
The army's Explosive Ordnance Disposal unit was called to the scene and a cordon was put in place for a time.
North Wales Police said it was "not a terrorist related incident".

Humberto Benitez Trevino's daughter caused outrage by using his influence to try to close down the bistro after it did not give her a table she wanted.
The episode sparked a discussion about abuse of power in the country.
The sacking suggests that Mexico has grown more sensitive to the issue, correspondents say.
The episode became a trending topic on Twitter under the hashtag #ladyprofeco, after her father's agency.
Mt Benitez, the attorney-general for consumer protection, and his daughter both apologised, but this did little to appease public anger.
On Wednesday, President Pena Nieto ordered his dismissal.
The restaurant, Maximo Bistro in Mexico City, was raided by officials after Andrea Benitez was not offered the table she had asked for.
The government said that although Mr Benitez was not personally involved in the raid, the episode had become embarrassing for the institution.
Controversial proposals to shut a Catholic school in East Dunbartonshire are to be examined by the Scottish government.
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A Wrexham street has reopened after police carrying out a search warrant found suspected firearms and "unstable" firework.
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Mexican President Enrique Pena Nieto has fired a senior official over an incident caused by his daughter at an exclusive restaurant last month.