Delays in setting national frameworks and guidelines for area teams has left a scattergun approach to practice payments and services.
GPC deputy chairman Dr Richard Vautrey said there were 'widespread concerns' from GPs that NHS England's 'unhelpful' approach meant they could not plan and did not know how they will be running their practices.
In some areas, decisions by area teams have threatened serious cash flow problems. Practices in south London received court summonses because they were unaware they were now responsible for paying business rates worth up to £120,000 a year, previously paid directly by PCTs.
Practices are still entitled to reimbursement of the rates, but the area team in south London told practices this could only be made over 12 months, even though councils were demanding upfront payment.
The area team for south London eventually reversed its stance after pressure from LMCs.
But NHS England said decisions on business rates would still be left to area teams. A spokeswoman said: 'Area teams are not bound by the arrangements established by each of the predecessor PCTs.'
Merton, Sutton and Wandsworth LMC chairman Dr Andrew Murray told GP the decision by the area team would have caused serious problems. 'For our practice, it is £30,000 a year. With that much, being reimbursed over 12 months is quite a big cash flow problem.'
Meanwhile, a decision by the West Yorkshire area team not to offer funding for locum superannuation contributions to PMS practices was condemned by Dr Vautrey. He said the decision would 'call into question whether PMS practices would be able to pass on superannuation payments to locums'.
GMS practices have been handed funding worth about £1,500 per practice to cover locum superannuation costs - a sum GP leaders say could leave some practices facing five-figure losses.
But NHS England looks likely to allow its local area teams to decide whether to offer PMS practices equivalent funding.
Dr Vautrey, a Leeds GP, said PMS practices were 'rightly angry' at NHS England, which gave the impression of being in 'chaos'.
In a further sign of NHS England's localised approach, area teams were told that services such as staff occupational health, maternity and paternity payments, sickness payments and retainer and returner schemes were 'potential QIPP (quality, innovation, productivity and prevention) opportunities' for cuts.
Area teams have begun cutting occupational health funding previously covered by PCTs (see page 16).
Dr Vautrey said while there were widespread variations under PCTs, it was taking too long for NHS England to develop a national approach. He urged area teams to 'maintain the status quo rather than making further cuts in an arbitrary way'.