East Dunbartonshire Council had decided that Auchinairn and Woodhill schools, as well as a learning and childcare centre, would be closed and be replaced by a new-build facility in Bishopbriggs.
The proposals, under the authority's Primary Schools Improvement Programme, drew an angry response from many parents who accused the administration of putting cost-cutting ahead of the educational needs of children.
While another proposal to close two primary schools in Lenzie and replace them with a new facility has been approved by Scottish ministers, the decision to merge Auchinairn and Woodhill has been "called in".
This means further investigations will be carried out before the Government decides whether or not to approve the plan.
Concerns were raised by the Government that the authority may not have fully addressed the impact the closure of Auchinairn Primary would have on the local community, which is classed as an area of deprivation, and that the planned replacement school could be too small.
It has also asked for more information on plans for traffic management around the proposed new school, as well as how out-of-school activities and childcare would be facilitated.
In addition, the Government has called on the council to explain why a policy guaranteeing maximum class sizes was reversed after a consultation was closed.
Debbie Gribbon, who has two daughters currently at Woodhill Primary and set up the campaign to save the school 14 months ago, said she was thrilled after hearing of the Government decision.
She said: "It's not very often that these things get called in, although we're still in a state of limbo as to what the next step will be. We feel we have a really strong case. They've found big issues they can't bluff their way out of.
"They [the council] asked our opinions but we've been completely ignored. This feels like a win in part but we'll see what happens at the next stage."
The council will now attempt to persuade the Government of the merits of its plan, which could still go ahead, be waved through with conditions or be thrown out.
An estate review of primary schools in East Dunbartonshire began in 2012, with a consultation launched last year.
Several schools could be shut as part of the wider shake-up which the council says is a response to falling school rolls, building maintenance costs and budget cuts.
Bearsden Primary School, which serves one of the UK's most affluent areas, had also been in line for the axe. It was spared after a high-profile campaign supported by Gruffalo author Julia Donaldson, who sent two of her children to the school, as well as ex-pupils Mark Knopfler, the Dire Straits guitarist, and Pop Idol star Darius.
SNP East Dunbartonshire councillor Gordan Low, who represents Bishopbriggs South, said the authority was guilty of double standards when dealing with schools in different areas.
He said: "[Bearsden] is not an area that requires regeneration and we are supposed to target scarce resources at areas in greatest need. Auchinairn is one of the council's target areas for regeneration. I don't think you regenerate an area by closing down a school."
Council leader Rhondda Geekie said she was delighted the council's proposals for Lenzie would go ahead and pledged to work with the Scottish Government to explain its proposals for Auchinairn and Woodhill in greater detail.