Out-of-hours GP services are suffering because of a lack of funding from local health bosses, doctors say.
Family doctors no longer have to provide out-of-hours services
About half of England is served by GP co-operatives - groups of doctors and nurses who cover nights and weekends.
The co-operatives say they are being under-funded by about 10% a year and want primary care trusts' (PCTs) spending on them to be investigated.
The NHS Alliance, representing PCTs, said it had warned previously they were short of money to fund co-operatives.
The co-operatives took on the out of hours service last year after most GPs opted out of providing cover under a new contract.
The National Association of GP Co-operatives (NAGPC) said that it costs between £5 and £15 a head each year to provide the service run by the teams, which are operated on a not-for-profit basis.
The association also claimed some co-operatives were being paid late.
NAGPC chairman Dr Mark Reynolds said: "There are a number of co-operatives which are suffering cash problems - either they are going to have to cut back on the quality of services or they are going to fold.
"It is important to remember we are providing a service of remarkably good value and if we can't provide the cover, people will use accident and emergency departments and that will cost the health service more."
One co-operative in North Yorkshire has already folded after having a request for more money rejected.
Dr Reynolds said he was going to write to the National Audit Office to ask for an investigation into the way co-operatives are funded.
The rest of the country is served mainly by internal PCT teams, although there are a small number of private firms which provide out-of-hours cover.
Dr Michael Dixon, chairman of the NHS Alliance, which represents PCTs, said difficulties were to be expected following change.
"We are bound to have teething problems but this is an issue we need to address," he said.
"We warned at the start of this process that PCTs were on average £250,000 short to fund the service."
But he said the problems should be sorted out over the coming years as the government is increasing funding for PCTs and he also expected more PCTs to rely on nurses and paramedics, which cost less than GPs.
Chris Town, a negotiator for NHS Employers, which also represents PCTs, added: "Primary care trusts have a balancing act. They need to make sure that out-of-hours services are high quality and they have to make sure that they get the best value for money."
Health Minister John Hutton said the government was committed to ensuring "every patient in the NHS has access to round-the-clock, 24-hour cover."
He said PCTs had sufficient money for out-of-hours cover as the government had increased funding by £300m.
And he added: "I do not see evidence that it [the new system] is not providing a quality service for patients."
The NAO said it would consider the co-operatives' request for an investigation.