Dr Malcolm Ward, chairman of the RCGP's rural forum steering group, said the plans would create problems for all GP practices. But they would be 'more extreme the more rural the practice', he said.
In the forum's response to a DoH consultation, Dr Ward said getting rid of practice boundaries will mean urban practices see a sudden increase in list size.
'This may put a strain on rural practices whose numbers become less viable, yet the remaining population will be the needy, sick, frail and elderly,' he said.
The proposals represented a 'sledgehammer to crack a nut' approach, which will fragment patient care, Dr Ward said.
The DoH consultation, launched in March, sets out four possible options to offer patients more choice.
These include allowing patients to register with any practice, but distinguish between local patients and patients registering further away; maintaining the requirement on GPs to make home visits to all patients, regardless of where they live; allowing people to register with two GP practices; or making PCTs responsible for home visiting arrangements.
But Dr Ward added that all of the proposals would increase the demand on ambulance services and secondary care.
'The patient who chooses to register with a distant practice, but becomes suddenly ill is likely to rely on emergency services rather than attend the chosen distant practices,' he said.
Dr Ward said there were 'more practical and cost effective solutions'. PCTs could be given the power to encourage practices to have more flexible boundaries in areas where there are problems, or incentivise practices to provide extended hours where there is a need.
He added: 'There are already options in place to cater for the needs of the working well who want to choose when and where they consult a GP, such as walk-in centres, or extended GP surgery hours.'