In a letter to NHS England, the BMA's GP committee has called for GPs and primary care networks (PCNs) to have in effect a power of veto over decisions to merge CCGs.
The number of CCGs has already dropped from 211 in April 2013 when NHS England became operational to 191 at the start of the current financial year - a fall of more than 9%.
This decline could be set to accelerate rapidly under NHS England's long-term plan, which suggested that in future there could be a single CCG for each emerging 'integrated care system' (ICS) area. These are expected to 'grow out of' sustainability and transformation partnership areas - of which there are just 44 across England.
In the letter to NHS England, BMA GP committee chair Dr Richard Vautrey said the union had 'heard from members who are extremely alarmed that mergers appear to be rapidly moving forward in their areas without clear approval from, or sufficient engagement with, local GPs'.
He warned that rules around CCGs needing to seek approval from local practices and GPs before going ahead with mergers had been 'watered down'. The GPC view was that 'such mergers should only be sanctioned if CCGs can clearly demonstrate that approval has been obtained from local member practices and primary care networks (PCNs)', Dr Vautrey added.
The GPC chair warned that creating larger CCGs through mergers could undermine local GPs' influence and ability to use their expertise to support good commissioning. He added that major changes to CCGs could undermine their existing relationships with practices and create doubt over whether funding agreements would be honoured or maintained.
Dr Vautrey also raised concerns that CCGs were being forced into mergers by cuts to their running costs - potentially at the expense of quality. He wrote: 'GPC England is extremely concerned that mergers are being rendered necessary and unavoidable by virtue of the 20% reduction in CCG running costs set out in the long-term plan.
'GPC England strongly opposes mergers going ahead motivated by cost savings: high quality commissioning, provider support and continuity of care must be always be prioritised over financial targets.'
An NHS England spokesperson said: 'Commissioners are indeed required to reduce their administrative costs by 20% and all savings are being reinvested in local health services.
'CCGs are therefore right to look for efficiencies, while at the same time individual GP practices also have the opportunity to work closely with their primary care network on strengthening local GP and primary care services.'