One in three GPs who are running new organisations that are about to be given £65bn of the NHS's budget also help run or hold shares in a private healthcare firm, a study shows.

The disclosure has sparked concern that such widespread conflicts of interest will threaten patients' trust in GPs, who they may see as lining their own pockets out of public funds.

Overall 426 (36%) of the 1,179 family doctors on a board of one of the 211 clinical commissioning groups (CCGs) in England have an interest in for-profit firms, including those providing common NHS services such as diagnostics, minor surgery and out-of-hours GP care, an investigation by the British Medical Journal (BMJ) found.

Some of them are senior directors of such firms, while others have a shareholding in major private health companies such as Harmoni and Circle Health, which already earn hundreds of millions of pounds a year for doing NHS work alongside local doctors.

CCGs represent all the GP practices in an area and most of their boards are dominated by GPs, although other kinds of doctors and patient representatives are also on them. Most of the key roles in CCGs are being discharged by GPs too.

The BMJ discovered that in some CCGs most of the GPs on the board have a financial interest in a local private provider of NHS care which the CCG, as the new commissioner of health in the area, may decide to hand a contract to after 1 April. On that day CCGs will become key bodies in the NHS as a result of the coalition's radical restructuring of the health service. From then they, rather than primary care trusts, which face abolition, will decide who should provide £64.7bn a year of healthcare for England's 60 million patients.

For example, six of the eight GPs on the board of Blackpool CCG have an interest in Fylde Coast Medical Services, the local out-of-hours provider. Amanda Doyle, the CCG's chief clinical officer, said most GPs on the board would have to "step away" if the overnight and weekend care service was being re-tendered.

Similarly, seven GPs on the board of NHS Leicester City CCG have a financial interest in the Leicester, Leicestershire and Rutland Provider Company.

And two of the three GP board members of NHS Chiltern CCG in Buckinghamshire are shareholders in a local profit-making company called Chiltern Health.

The BMJ obtained the registered interests of board members of 176 of the 211 CCGs through freedom of information requests and searching their websites. It found that 555 (23%) of 2,426 clinical, lay and managerial members of CCGs' governing bodies – almost one in four – had a stake in a private operator of some sort.

In addition, 4% of GPs on CCG boards were consultants to or advised private health firms or pharmaceutical companies; 5% worked for a private health firm as well as working as a GP; and 9% declared a conflict of interest arising through a family member.

Last October Virgin Care said it was ending its joint venture partnerships with about 300 GPs across England because many of them were becoming "increasingly worried about the perception of potential conflicts of interest".

The revelations prompted the Royal College of GPs (RCGP) and British Medical Association (BMA) to warn that high public trust in GPs could be jeopardised by family doctors having private healthcare interests while also working as GPs in the NHS.

"If conflicts of interest in clinical commissioning groups are not managed effectively, the consequences could badly undermine the confidence of regulators, providers and, most importantly, patients, in the system," said Dr Clare Gerada, chair of the RCGP.

Members of CCGs should disclose details of any conflicts of interest they find themselves in and "exclude themselves from decision-making where a conflict of interest exists. But there should be prompts and checks to reinforce this and rules to ensure that decision-making is efficient, transparent and fair, without being overly complex or slow," she added.

Dr Laurence Buckman, chair of the BMA's GPs committee, said that while the doctors' union supported the principle of clinicians being involved in commissioning, "it must not come at the expense of the trust of patients". Stronger safeguards are needed, he added.

Some leading GPs privately fear that these conflicts of interest, coupled with GPs becoming responsible for rationing access to treatments and CCGs' ability to pay local GPs bonuses in the form of a "quality premium" for meeting certain targets, could cause tension with patients and see some of their decisions lead to negative media coverage.

Labour warned that board members' links could see the private sector gaining a bigger role in the NHS. "These revelations will fuel growing fears about the back-door privatisation of the NHS arising from the government's re-organisation," said Andy Burnham, the shadow health secretary.

"Patients and public want those entrusted with making decisions about the NHS to have its best interests at heart. They will be shocked to learn that so many have a potential conflict of interest," he added.

A code of conduct drawn up by the NHS Commissioning Board, which oversees and funds CCGs, says board members should not be involved in decisions from which they could ultimately make money. It expects to "shortly" publish statutory guidance to CCGs on managing such situations, a spokeswoman said.

But Dr Michael Dixon, the interim president of NHS Clinical Commissioners, which represents 130 of the 211 CCGs, said boards should be trusted to act properly.

"While it is right that potential conflicts of interest are identified, they can be managed with appropriate openness and transparency; the fear of perceived conflicts of interest must not become a dead-hand stopping new and innovative service development and the ability of CCGs to deliver services in new settings", he said.

• This article was amended on 21 March 2013 to remove a statement that the BMJ had found that five GPs on the board of Blackpool CCG have an interest in Virgin Care. The BMJ has since clarified that that the interests registered in Assura Blackpool – the limited liability partnership jointly owned by Virgin Care and local practices – were held through the GPs' practices, not individually, and that the local practices in question have now resigned from Assura Blackpool.