Dr Peter Swinyard told MiP the CQC GP registration and compliance criteria will only serve to "annoy the entire profession".
"The public will fight tooth and nail to support GPs," he said.
He also warned the CQC will find itself on a "sticky wicket if it tries to mess with practices".
Dr Swinyard said the regulator "hasn't got a chance" of adding value to general practice and doubted its inspectors' knowledge in carrying out the tests and checks required.
In a statement to MiP, Professor David Haslam CBE, the CQC's National Clinical Advisor, said the regulator has no intention of "messing with practices" or "undermining" the work of GPs.
"It is a legal requirement to register with the Care Quality Commission, however registration with us is not designed to undermine the valuable work that GPs do but to provide assurance to the public that every aspect of care from hospitals to care homes is regulated under a single set of essential standards for the first time," said Professor Haslam.
"The role of our inspectors is not to look at the clinical practice of individual GPs. The Government requires CQC to look at the whole practice, to ensure that areas such as hygiene and cleanliness standards are maintained and people's dignity and rights are respected and that is what our inspectors are trained for.
"Our role will not be to "mess with practices" we are fully aware that the vast majority of practices are delivering good quality, safe care and will be meeting the essential levels of quality and safety already. We are currently working with the sector to make sure the process is as streamlined as possible The Family Doctors Association is fully involved with our advisory group helping us plan and design what regulation will look like."
The FDA chair's comments come as it is claimed more than 1,000 practices in the UK have signed up to use software designed to help them prepare for Care Quality Commission (CQC) compliance.
In a series of myth-busting questions posed to the CQC by the FDA last month, the CQC said "PCTs should not be telling practices to do things in the name of CQC" before GP regulation commences from April 2013.
It said it plans to take action against those PCTs that are proved to be continuing to do so.
Your comments (terms and conditions apply):
"Nurse led with non evidenced standards borrowed from secondary care it is a fruitless endeavour which will do little to improve patient care. It is possible it may worsen some aspects of patient care as the fairly lean primary care administration is diverted into poorly though out compliance criteros" – R Burley, BFPO
"It now seems inevitable that GP practices will have to be regulated with the CQC as most other providers now are registered or will be by 2012. But it is not as onerous as process as it seems. Take a good look at the standards – all well run practices will see that they are meeting those already. Big NHS trusts did not use complex software or external consultants to successful achieve compliance in 2010. What is required is a coordinated approach across practices to assess current systems and processes to identify gaps in compliance, to develop a plan to address the gaps and to ensure that systems are in place to confirm compliance at all times. Practices will surely have robust systems already in place to qualify for QOF points" – Siobhain O'Donnell, Kent