The Scottish Government said it was reviewing the decision to close St Joseph's Primary in East Dunbartonshire, claiming consultation documents potentially included inaccurate data relating to the cost and savings of closure and creating a new facility, and how rolls were calculated.
It also claims East Dunbartonshire Council failed to address the concerns raised by Education Scotland that St Joseph's pupils would lose the advantages they currently receive "both within the school and in its community location".
The move gives the Milngavie primary a stay of execution, with parents who have fought a long campaign against the closure plans claiming they are now hopeful it will remain open.
An official consultation by East Dunbartonshire found the vast majority of those who responded were against the proposal.
The school, which the council plans to merge with St Andrew's Primary in Bearsden, is the only Catholic primary in Milngavie.
An assessment of the impact on equalities legislation by the council even suggested the proposal could be considered to be indirect discrimination against Catholic families in Milngavie.
Confirming the "call-in" to the authority's head of education, the head of the Scottish Government's school infrastructure unit cites concerns the running costs of St Joseph's may have been over-estimated and the full costs of the proposed new school not provided.
It was also claimed the council consultation document may not have fully reflected local opposition, and calculated under-occupancy differently to other schools in the area.
It adds: "As such the proposal may have proceeded on a flawed or inaccurate basis, which may suggest a potential failure in a significant regard to comply with the requirements imposed on the council in relation to the closure proposal.
"There are concerns that the consultation report did not fully reflect or have regard to the level of opposition to the proposal."
Laureen McIntyre, chairwoman of St Joseph's Parent Council, said: "It's clear the way East Dunbartonshire has conducted its consultation process has more holes than a colander. Councillors have based important decisions on information containing serious factual errors.
"Our local representatives should reflect on the fact this could've been avoided if they'd listened to our community instead of ignoring us.
"Putting our children on a bus to Bearsden and removing them from the support of a vibrant local community makes no sense to anyone. St Joseph's Primary is a fantastic school with the fastest-growing roll in the whole of East Dunbartonshire."
East Dunbartonshire Council leader Rhondda Geekie said: "This is a complex process and it's understandable that the Scottish Government wants to investigate the proposal further.
"We have been through the same process with them for Auchinairn and Woodhill primary schools earlier this year, which concluded with the new school build going ahead for Bishopbriggs as proposed by the council."
A Scottish Government spokesman said: "Ministers will now consider all available material relating to the proposal in order to determine whether or not to give their consent to it."
The call-in was also welcomed by the Archdiocese of Glasgow.