Practice leaders are being urged not to be swayed on CCG size by the perceived "low" value of the management allowance.
The Clinical Commissioning Coalition said any suggestion there is a one size fits all model that CCGs should adhere to is "setting the clinican-led reform up to fail".
The call for CCG independence comes as speculation grows that the £25 management allowance, set by the government in its 2012-13 NHS Outcomes Framework, will force CCGs to merge into PCT-like organisations.
Chair of the NHS Alliance Dr Mike Dixon said it is "absolutely fundamental" CCGs are free to make their own decisions on configuration details if they are to ensure a local and patient-centred NHS.
"Although we understand concerns around the current £25 management allowance, patients come first," he said.
"CCGs are there to create a health care system that focuses on local needs, is patient centred and led by clinicians."
Dr Johnny Marshall, Chair of the National Association of Primary Care (NAPC), said there is a danger CCGs will "miss the point of the health reforms" if they grow in size to meet the management allowance challenge.
In his letter to GPs, Dr Laurence Buckman, Chair of the BMA's GP Committee, said the proposed management allowance is not "sufficient" to allow CCGs to function effectively.
He said the GPC will be seeking a "substantial increase" in the figure.