Mall operator Intu won permission to add 11,000 square metres of floorspace to its Midsummer Place centre in September as part of a scheme that would also extend its footprint.
Milton Keynes Council planning officers had recommended the scheme for approval despite objections that it breached policies in the recently-made Central Milton Keynes Business Neighbourhood Plan.
In a report to councillors, officers recognised tensions with policies on preserving "classic Central Milton Keynes infrastructure" and semi-public open space, but found that "on balance" the proposals complied with the neighbourhood plan.
Both Central Milton Keynes Town Council, which produced the plan, and its adviser David Lock - founder of consultancy David Lock Associates - said the decision undermined the purpose of neighbourhood plans and urged Clark to call the case in for further scrutiny, using powers in the Town and Country Planning Act 1990.
Lock said it was vital for the weight attached to the business neighbourhood plan by the local planning authority to be tested at a public inquiry.
"There is a profound point of national interest at stake here," he said. "If this decision stands, neighbourhood plans of any type are rendered pointless; the Localism Act is hollowed out."
Intu told Planning it was disappointed that the Milton Keynes proposals had been called in by Clark. Regional director Martin Breeden said a "significant majority" of councillors on Milton Keynes’ development control committee had decided that the application was in accordance with the neighbourhood plan.
"It will now be for central government officials to determine whether or not planning permission should be granted, taking this important decision away from the people of Milton Keynes," he said.
"This will delay our proposed investment in new shops, restaurants, leisure and local jobs, which we believe will be to the detriment of Milton Keynes."
Milton Keynes Council did not respond to Planning’s request for comment by the time of publication.