Hundreds of practices across England face potential disputes over the charges because they have no signed lease agreements with their PCT.
Failure to pay up could see practices in PCT-owned premises taken to court, or face visits from bailiffs or even eviction.
Londonwide LMCs' medical director Dr Tony Grewal described the situation in the capital as 'chaotic'.
'Some PCTs are pulling service charges out of thin air,' he said. 'There is one for £100,000 going back over 10 years. In general they are £10,000 a year, with most going back one to three years.'
Dr Grewal said he knows of three London practices that have been 'vigorously approached' by debt collectors. He said these cases had yet to reach the level of threats or bailiffs.
GPC negotiator Dr Peter Holden said: 'If there is nothing in writing that says you have to pay a service charge, then there is nothing to pay.'
If, however, a written agreement exists but the PCT has been 'too idle' to collect fees, practices can negotiate a payment period but must ultimately pay up, he said.
One London practice, according to Dr Grewal, was initially given just 30 days to pay.
Lynne Abbess, a partner at specialist medical solicitors Hempsons, warned that PCTs could 'in theory' threaten to evict practices if they do not comply and where they do not have a signed lease agreement.
'The PCT may adopt the position that it has the power to throw them out of the health centre as they have no legal right to remain, although this is likely to be capable of legal challenge,' she said.
A spokesman for the Outer North East London PCT cluster said that none of its four PCTs had hired a debt collector to claim back service charges. The rest of the capital's PCT clusters did not respond.
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