The 11,000-patient Hillside Practice in Skelton moved into a new PFI building in March, with the support of Redcar and Cleveland PCT.
The practice made the move in the expectation that it would expand to serve the village's growing population.
But the PCT is now classed as under-doctored and is to host two new APMS practices.
The plan includes a new 3,000-patient practice in Skelton, less than half a mile from Hillside's current location in its 'cramped' old building.
The move comes despite a public consultation which overwhelmingly rejected plans for a new practice in the village.
Dr Kate Harvie, one of the practice partners, said that she believes the PCT has chosen the site purely because a building is available.
'We're very concerned,' she said. 'It either won't work and will be a huge waste of money, or it will be a success and destabilise us.'
She added that the practice's building overheads have increased 'several times' thanks to its PFI costs.
The partners at Hillside say that, if the practice loses 3,000 patients, it will have to reconsider its staffing levels and GP numbers.
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