Just weeks after MK Council voted through planning permission, the Secretary of State has called the matter in for further investigation.
He has ruled that a public local inquiry will be held before a final decision is made.
The proposed multi-million extension sparked local protest because part of it involved land identified as public open space in the CMK Business Neighbourhood Plan.
The plan had been voted through by 90,000 residents in a referendum earlier this year and the intu extension would be a direct contravention, said objectors.
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But at a heated planning meeting in September, councillors agreed by ten votes to two to allow the development to go ahead.
The extension would include a boutique cinema, restaurants and more shops.
The Secretary of State’s intervention could now force the scheme to be scrapped or delay it for up to two years.
Intu bosses say this will be a economic blow for Milton Keynes as it will delay their investment and the new jobs the expansion would provide.
The planning application was opposed by Tory councillor John Bint, who told the Citizen at the time: “I am absolutely convinced this application contravenes our policies.”
The council’s decision was called in by CMK Town Council, whose chair Rebecca Kurth said: “There is a principle at stake here. We were told the neighbourhood plan would give local people and businesses power over the future of development in their area - and the council has turned round and ignored it.”