Handing GPs control of the health budget and commissioning of hospital services would be "disastrous", a medical charity has warned.
Health Secretary Andrew Lansley believes family doctors are best placed to understand patients' needs and wants them to decide where money is spent.
But a Muscular Dystrophy Campaign study seen by Newsnight found many GPs had no knowledge of muscle-wasting conditions.
This would result in inappropriate referrals, the charity says.
The research comes as Unison launched legal action against the government's plans for a major shake-up of the NHS system in England.
The UK's largest public service union claims ministers failed to ask the public if it wanted such fundamental changes in the first place.
Currently, about 80% of the £100bn annual NHS budget is given to local health managers working for 152 primary care trusts, which in turn commission services for their areas.
The proposals in the health White Paper would hand the responsibility for commissioning most of these health services to groups of GP practices that would work together in consortia - a move long championed by Mr Lansley.
Our report has shown exactly why GP commissioning of specialised services cannot work for patients with rare diseases, and we would urge the government to consider very carefully the impact this reform could have
Muscular Dystrophy Campaign
But the Muscular Dystrophy Campaign's research for its State of the Nation report found almost 50% of 650 patients surveyed did not receive a correct or prompt diagnosis from their GP.
More than half said they felt GPs did not have a good understanding of muscular dystrophy and almost a third said they were not correctly diagnosed for more than five years - with one patient waiting 68 years.
The charity's report also concluded that millions of pounds spent on admitting people to hospital could be saved if a small amount of it was invested in specialist care for the condition - such as physiotherapy.
The Muscular Dystrophy Campaign's acting chief executive, Robert Meadowcroft, said these patient experiences confirmed "how disastrous a move to GP commissioning could be".
"Neuromuscular services have been neglected for years and this could make the situation even worse," he said.
"It is unacceptable that a patient should be delivered such a devastating diagnosis and then not offered the best possible care and advice straight away, or in some cases not given a definite diagnosis at all."
He added: "Our report has shown exactly why GP commissioning of specialised services cannot work for patients with rare diseases, and we would urge the government to consider very carefully the impact this reform could have."
About 70,000 children and adults in the UK have muscular dystrophy or related conditions, which cause muscle weakness or wasting.
Jane Field, from Droitwich, said her 12-year-old son Murray was misdiagnosed on two separate occasions.
"I never go to see our GP - why would I? I know far more about the condition than they do. GP commissioning would be catastrophic."
When GP consortia take responsibility for commissioning, specialised treatment such as this will remain in the hands of specialists
Dr Laurence Buckman
British Medical Association's GPs Committee
But Dr Laurence Buckman, chairman of the British Medical Association's GPs Committee, said the Muscular Dystrophy Campaign's fears were unfounded because the commissioning of treatment for such rare conditions would remain the responsibility of specialists.
"Muscular dystrophy is a rare and distressing condition. There are very few people in the NHS, including GPs, who have expert knowledge of it," he said.
"This is why, when GP consortia take responsibility for commissioning, specialised treatment such as this will remain in the hands of specialists and will not take place in the way the Muscular Dystrophy Campaign fears it will."
He added: "Patients with muscular dystrophy deserve specialist advice and care, and GP consortia will want to ensure that they get it."
A spokeswoman for the Department of Health said GPs would act as "expert guides" through the health system, but would not be working alone.
"In this role, GP consortia will work closely with secondary care, community partners and other health and care professionals to design joined-up services that are responsive to patients and the public," she added.
Responding to Unison's legal challenge to the government's White Paper, the department said the government was engaging fully with the public, healthcare professionals, local authorities and unions on how its proposals will be implemented.
The government's consultation on how the NHS changes would be implemented ends on 5 October 2010.