CCGs will need to rely on each other to broker sums of money to each other to cover end of year positions and 'overlaps' in services.
Former Labour MP for Dartford, Bexley CCG Chair Dr Howard Stoate told GPB his neighbouring CCGs in South East London have been "sympathetic" to his low funding allocation.
With a patient population of 230,000 spanning 28 practices, Bexley CCG is in the third quartile of CCG funding – unlike most other South East London CCGs who have found themselves in the top quartile.
He said low funding will force Bexley to work to three-year long projects – instead of making changes year-on-year.
"We haven't got the resources to allow the dual-running of services to make sure we have a seamless switch from one set of services to another better and more cost-effective set of services," he said.
"NHS South East London has been very flexible and is looking at how they can release transitional funding to help us fund the inevitable overlap of services.
"Post April 2013, we will have to rely on other CCGs to plug the gap."
Dr Stoate said the problem will affect many CCGs in the future and hopes a "fluidity" of funds between CCGs emerge.
"There needs to be the ability to move resources or share staff and expertise [around CCGs] to allow a particular bit of work to go on in one area for it then to flow back and be transferred elsewhere," he said.
"It is too early to say how that is going to happen but that is the broad way we are going."
Dr Stoate said he is not sure where the CCG £25 running allowance came from and said his preference would have been for a base allowance, in which every CCG gets a lump sum regardless of their size and then a capitation top-up depending on their population.
He claims that would have allowed smaller CCGs to be "more viable".
Speaking at the NHS Clinical Commissioners conference in London earlier this week (24 April), Health Secretary Andrew Lansley said CCG funding should be based on the age of its population rather than deprivation indicators.
While Dr Stoate said there isn't a formal merger on the cards between Bexley, Bromly and Greenwich CCGs – a claim backed up by Bromley CCG Chair Dr Andrew Parsons – he expects the three organisations will "inevitably pool their resources" and draw up one acute contract with South London Healthcare NHS Trust.