The Alma Road Primary Care Centre in Peterborough, Cambridgeshire, has been given six months' notice to close as the city's PCT looks to make savings.
APMS contracts contain a 'no cause' clause meaning the PCT can cancel the contract without giving any reason.
Dr Rupert Bankart, medical director of 3Well Medical, the GP-led firm running the health centre, said many more GPs would face the same fate.
'This is probably the first time an APMS contractor has been issued with a termination notice for no cause. It's dawning on us that the implications of this are significant for GPs across the UK, if APMS is now the preferred model of contract.'
According to data from 2009, there are 173 practices in England that operate under APMS deals, which allow non-clinicians to hold the contracts.
The recent White Paper Liberating the NHS signalled a move towards a single GP contract, which will include aspects of APMS.
The Alma Road health centre currently sits in a temporary building. It is one of 150 GP-led health centres built under the last government's plan to set up one in each PCT.
The BMA argued as the centres were being developed that they would be costly and surplus to requirements.
NHS Peterborough hopes to save up to £800,000 by closing the Alma Road clinic, claiming it duplicates other local services and has underperformed in registering patients. A permanent building for the practice, originally due to open this April, has been cancelled.
Dr Bankart said the practice had gone the 'extra mile', opening from 7am until 10pm every day, with its walk-in service operating at 140 per cent of the volume expected by the PCT, and a cost per head for registered patients lower than average for the area. The practice also believes its late-night walk-in service has significantly reduced A&E admissions, although the PCT refutes this.
The GPs at 3Well Medical say they have little grounds for appeal legally because they were unable to remove the 'no cause' clause during tendering. They hope the support of patients, local councillors and GP consortia may help their cause.
The DoH has said all major PCT decisions must be signed off by GP commissioners. A consultation on the closures runs until 29 October.