Supporters of St Joseph's, in Milngavie, have vehemently opposed plans to shut the school and build a new primary in nearby Bearsden.
Now the Scottish Government has announced it is "calling in" East Dunbartonshire Council's decision.
In a letter to the council, ministers said the consultation documents included inaccurate data relating to financial information and the way in which the under-occupancy rate was calculated.
The Scottish Government also said: "There are concerns that the consultation report did not fully reflect or have regard to the level of opposition to the proposal."
Chairwoman of St Joseph's Parent Council, Laureen McIntyre, said: "We welcome the Scottish Government's decision to stop the closure of St Joseph's and call-in the decision.
"I would like our local representatives to reflect on the fact that this could have been avoided if they had listened to our community, instead of ignoring us.
"St Joseph's is a fantastic school with the fastest growing roll in the whole of East Dunbartonshire. We belong in Milngavie and today's decision gives us hope that this is where we will stay."
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 primaries earlier this year, which concluded with the new school build going ahead."
While plans for St Joseph's are stalled, the council has said it will now move ahead with a scheme to merge two primary schools in Kirkintilloch and establish a new £7 million school for the town.
Some 300 St Agatha's and St Flannan's pupils will merge in a new build school at the current St Flannan's site, due to open in the school session 2016/17.