East Ayrshire's 52-pupil Crossroads Primary is the first high-profile case to be scrutinised since new legislation, which is designed to protect rural schools by ensuring a fair consultation process, came into force in April.
Campaigners for the school argued that consultation had not been handled as it should have been. The closure would result in pupils being sent several miles to Galston Primary and devastate the local farming community, yet consultation letters were sent home with children, they protested.
East Ayrshire Council said the run-down school, which was found to have structural problems, would have cost an unjustifiable pound;1.2 million to refurbish, although campaigners claim to have had a quote of about half that. Pupils have been educated at Bellfield Primary since last year.
In a letter to the SNP-run council this week, the Scottish Government confirmed that consultation obligations under the terms of the Schools (Consultation) (Scotland) Act had been fulfilled, paving the way for immediate closure.
Sandy Longmuir, chair of the Scottish Rural Schools Network, said the decision was "possibly a seminal moment in the future of Scotland's rural schools". They were now "in a far worse position than before the new legislation was enacted". He disputed any suggestion that the state of the school building made Crossroads an atypical case, adding that schools in need of refurbishment were now under greater threat in several authorities, including the Borders, Highland, Angus, South Ayrshire, Angus, Aberdeenshire and Moray.
Labour education spokesman Des McNulty painted the decision as a broken manifesto promise, after the SNP came into power in 2007 promising to fight for rural schools. But local SNP MSP Willie Coffey accused Labour of "hypocrisy" after pointing out that opposition Labour members of East Ayrshire Council had unanimously backed the closure of Crossroads.
The Government says that the act was never intended to stop all school closures, and its decision was based largely on educational benefits.
The council has already started planning for the move to Galston Primary. Pupils will remain at Bellfield when the new term starts, and transfer after the October break.