Northumberland LMC secretary Dr Jane Lothian said a PCT locally had failed to introduce the new local enhanced services in April, instead introducing them around four months into the financial year.
Concerns have also been raised about PCTs clamping down on payments as they try to make efficiency savings.
Dr Lothian said the problem had arisen because 'half the PCT has now disappeared', leaving an 'impossible burden' on remaining staff. 'When all the ground managerial talent has gone there is nobody left to do the work,' she said.
A spokeswoman for NHS North of Tyne said it is not aware of any 'significant delays' in sign up for enhanced services.
Dr Robert Morley, executive secretary of Birmingham LMC, said his PCT was 'micro-managing practices'. 'PCTs are looking to make easy savings through enhanced services and QOF performance,' he said. 'These are seen as easy pickings.'
'It seems we are having more and more practices that PCTs are looking at and more and more disputes. They seem to be going over everything with a fine-toothed comb.'
GPC deputy chairman Dr Richard Vautrey said he would be 'very concerned' if PCTs were using such tactics as cost-saving measures.
'We have heard stories from PCTs for a number of years where individuals have been nitpicking and obstructing payments,' he said. 'It's always a concern where PCTs make problems for practices.'