The warning from the Family Doctor Association comes amid growing disquiet among GPs over a move to switch £164 million of funding away from administrative duties to incentives for them to target certain medical conditions.
Dr Peter Swinyard, chairman of the association which represents more than 1,000 practices, said the changes would see smaller practices squeezed "until the pips squeak".
He warned GPs had no time to take on the new changes which would affect smaller surgeries the hardest.
He said: "The pips are squeaking in general practice and there is no room left for adding yet more work without adequate resources.
"Smaller practices will find dealing with these things much more difficult than most, because they haven't got the strength and depth of larger practices to spread the workload."
Doctors in the region have already expressed their own concerns, with a survey revealing fears that two-thirds of surgeries in the Westcountry may struggle to remain viable after the changes.
Peter Merrin, chairman of the Cornwall and Isles Of Scilly Local Medical Committee, said they shared the concerns of the Family Doctors' Association.
"The proposed contract imposition comes at a time when morale among GPs is falling as a result of the increasing demands of an ageing population with increasingly complex medical and social problems," Dr Merrin, a GP at Perranporth, said.
"In addition there is a steady transfer of work from the hospital sector into the community increasing the workload for all health workers in the community sector.
"We see the new contract as a threat to small practices and are urging family doctors to look at ways in which they may share some of their workload with other practices.
"This doesn't necessarily mean merging practices but it might mean better and smarter use of our resources. As yet we are unclear how this will impact on patients."
He added: "In Cornwall, we remain committed to providing high quality general practice to all of our patients but the ways in which we deliver that care may and probably will have to change as a result of increasing workload and the new contract."
Negotiations between the Department of Health and the British Medical Association on changes to GP working practices broke down late last year. Consultation on the Government's proposals has now closed and an imposed contract is likely to come into force from April 1.
The Department of Health has insisted that no money has been taken away from GPs and it had offered extra funding.
Ministers have argued that the changes will lead to fewer deaths from the main diseases and more cases of diabetes, dementia and other conditions being diagnosed earlier.
But Dr Swinyard said surgeries in rural areas which were small "by necessity" and those in towns and cities which were small "by history" would be affected.
A change to the way practices were paid to provide locums, he said, would also see smaller practices losing out.
The depth of doctors' concerns was revealed earlier this year.
Almost half of the 6,000 GPs in Cornwall, Devon, Avon, Gloucestershire, Somerset and Wessex responded to questions put by their Local Medical Committees (LMC).
Two out of three (67%) said their practice would "struggle to remain viable" if the changes went ahead while almost half (48%) said their current workload was "dangerously unsustainable".
Dr Mark Sanford-Wood, chairman of the Devon LMC, described the "personal GP system" enjoyed by patients as being "under serious threat from the Government's plans for the future".
Health Minister Lord Howe said it was considering the responses to the 12-week consultation and would "announce the outcome shortly".
"Our proposed changes to the GP contract are designed to improve the care offered to patients," he said. "The consultation – and hearing the views of GPs and other stakeholders – will help us decide how this can be achieved."
