Camden PCT has sent letters to all patients who have not visited their GP in the past year warning them they will be taken off the list unless they confirm that they are still living in the area.
The list-cleaning programme, which was piloted at three surgeries earlier this year, is a bid to cut the number of residents who have moved on but for whom GPs are still being paid.
The project has now been rolled out across the borough.
A spokeswoman for Camden PCT said letters were sent out in 17 different languages and that practices were given eight weeks to prove a patient did exist before their record was withdrawn.
But the PCT has come under fire from GPs who say the process is heavy handed.
Camden LMC chairman Dr Stephen Amiel said healthy patients who have not needed to see a doctor will be struck off the list if they miss the letters or have moved house and kept their GP.
'I don't think this is the way to go about it,' he said.
Dr Philip Matthewman runs a single-handed surgery in Kentish Town and was chosen by Camden PCT to pilot the programme.
He said a quarter of his 2,400 patients have been removed from his list.
Dr Matthewman said: 'It has caused anxiety for patients and a lot of hassle for our staff who have already had to re-register more than 100 of those taken off the list. Some patients are weary of responding to mail-outs.
'Our income has dropped by 25 per cent, which makes it hard for us to plan for the future.'
The Camden PCT spokeswoman said it delayed list cleaning while GPs got used to the new GMS contract, but that it was overdue.
She also said the high number of ghost patients skewed targets in areas such as childhood immunisation.
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