It means North Lanarkshire Council cannot proceed with its plan to shut Abronhill High, Cumbernauld, until Government ministers have gone over the proposals.
The council wants to close Abronhill High and move the 480 pupils to a new school, Cumbernauld High, which would to be built by 2016.
It says Abronhill's roll is falling, the school is almost half-empty and the closure decision will save £1.3m a year.
It was due to shut in June, but following a consultation the closure has been put back to 2014.
But in a letter to the council, the Scottish Government's School Infrastructure Unit, said: "Scottish ministers are concerned the educational benefits statement prepared by the council around their proposal lacks clarity about the benefits to be realised in the period before a new school is built."
The Evening Times revealed last week that the Scottish Government had received a record number of almost 800 requests for a call-in on the decision. And parents said they were pleased by the latest development.
Pete Reid, 47, is a member of the Save Abronhill High School group and his two daughters attend the school.
He said: "We are thrilled the Government has called in the council's decision.
"All along we have we felt there has been some fundamental areas the council has not properly addressed, that the council was not telling the community the whole story."
Cumbernauld and Kilsyth MSP Jamie Hepburn was also overjoyed at the Government's action.
He said: "This does not definitively shut down the plans advanced by North Lanarkshire Council, but it is clear ministers recognise the council has to answer the serious questions and concerns posed of it.
"It will be interesting to see how it tries to justify its plan to ministers."
The council accused the Government of overlooking the educational needs of pupils.
Jim Logue, convener of Learning and Leisure Services, said: "Clearly, this (call-in decision) has been driven by political considerations rather than in the best educational interests of the young people attending the schools concerned.
"The schools are hugely under-occupied and, as an educational authority, we have already seen the benefits of merging under-occupied secondary and primary schools and providing pupils with wider educational opportunities.
"To be clear, this is not solely about money, although we cannot continue to heat, light and maintain empty classrooms.
"This is about providing better opportunities to our young people now and for generations to come.
"The reasons given by the Scottish Government for the call-in do not stand up to any scrutiny and we are 100% confident of our position."