GPs preparing to take charge of £60bn of NHS funds have been found to have shareholdings in private healthcare firms, prompting alarm about family doctors profiting from direct conflicts of interest.

Fresh research shows that in 22 of the new clinical commissioning groups (CCGs), at least half and sometimes all of the GPs that dominate their boards have a personal financial interest in a private or other non-NHS provider.

In 10 CCGs, a majority of GP board members belong to a local "provider company" they help run as a partnership with Virgin Care, which makes profits by being paid by the NHS to offer dermatology, physiotherapy and rheumatology services.

In seven other CCGs, many of the board-level GPs receive a second income from providing out-of-hours care in the area as members of not-for-profit family doctor collectives.

Doctors' leaders warned that such conflicts of interest could anger patients, diminish trust in GPs and lead to more NHS services being taken over by private operators.

"The fact that GPs have these outside interests may influence their commissioning decisions, and may put at risk their relationship with their patients because the patient might mistrust where they are being sent to for treatment and the GP's motives", said Dr Clare Gerada, chair of the Royal College of GPs.

"It may also damage the NHS because having many different providers will increase costs and fragment care, which means patients will lose out."

Johnny Marshall, chairman of the National Association of Primary Care and one of the few official advocates for the NHS overhaul, admitted GPs performing both roles could cause problems.

"It's really important as a public body from a conflicts-of-interest point of view that we end up operating above reproach and suspicion. We can't find ourselves in the position where there's a perception among patients that the decisions we are taking about their care are influenced by personal financial gain."

Marshall called on ministers to use the 12 months before the new NHS set-up starts to ensure tough mechanisms, consistent with the Nolan principles used elsewhere in public life, are put in place to avoid problems.

Virgin Care says clear policies and procedures are in place to manage any conflicts of interest that arise. "All GPs are providers of care first and foremost," a spokesman said. "This means that in fulfilling their new commissioning responsibilities all GPs are exposed to a potential conflict of interest – whether as a partner in their own practice or in provider organisations.

"In order to manage any potential conflicts of interest effectively there are long-standing policies that have been advocated by the Department of Health, the Royal College of GPs and the BMA. These are regularly updated to ensure the highest standards of corporate governance and are adopted by our GP provider organisations."

The health and social care bill that enshrines the new clinical commissioning groups finally became law on Tuesday, receiving royal assent after 14 months of political intrigue. Labour MPs shouted "shame" when the news was announced in the Commons.

It came soon after the leaking of the Department of Health's risk register, which identified potential dangers in the NHS shakeup such as that the service could manage emergencies less well in future, and that GPs lack the skills to run the new clinical commissioning groups.

CCGs will become powerful new bodies in April 2013 as a direct result of the coalition's NHS shakeup when they replace primary care trusts (PCTs) across England as the commissioners of care and gradually assume control of £60bn of the health service budget they will be handed to pay for patients' treatments.

The revelations have prompted concern that doctors who both sit on CCG boards and own stakes in non-NHS providers could use their decision-making power to simply commission their own companies to offer care.

At the moment both "provider companies" and GP out of hours collectives do so under contracts from local PCTs. The fear is that while some doctors currently make money from involvement in either type of set-up by acting as a provider of care, those who also sit on CCG boards could benefit by also acting as commissioners of healthcare -- and using their decision-making power to favour firms they have links with.

The 22 CCGs have been identified by False Economy, a research group funded by the TUC. It examined publicly-available details about the board members of about 50 CCGs, identified which are GPs and then established what financial interests they had beyond their usual work at their surgery. It found that in 22 CCGs at least half the family doctors on the board have an outside financial interest.

A False Economy spokesman said: "The risk revealed by our findings is that GPs who formed provider companies in good faith, in response to government policy, and often on a cooperative basis, find themselves accused of trying to profit from GP commissioning by rival bidders – often big health firms with private equity backers looking for any opportunity to muscle in on local health services."

All six GPs who make up the board of Bath and North East Somerset CCG work at surgeries which are members of a local GP-Virgin Care partnership, Assura Minerva. It provides fracture clinics, private minor surgery and help for those with deep vein thrombosis, among other services.

A spokesman for NHS Bath and North East Somerset PCT insisted that GP board members would not be involved in decisions which could see a firm in which they have an interest being awarded a contract. However, this would mean that all the six GPs would be barred from voting on any tender that Assura Minerva was bidding for, raising serious questions about the CCG's ability to make a decision.

Virgin Care said that it had procedures in place to deal with such a situation, for instance bringing in a neighbouring CCG.

Assura Minerva was part of Assura Medical, which recently changed its name to Virgin Care. A Virgin Care spokesman confirmed that while a few of their 25 joint ventures with GPs put their profits back into patient care, others do not, and that the impending extension of competition into the NHS resulting from the NHS overhaul could lead to some of their 25 partnerships bidding to provide more services.

A Department of Health spokesman said: "We strengthened the health and social care bill to set out what CCGs must have in place to manage conflicts of interest. There will be a requirement for clinicians to declare and publish potential conflicts of interest and for CCGs to ensure transparency and integrity of their decision making. The NHS commissioning board, as part of the authorisation process for CCGs, will also make sure that each group has clear arrangements in place to manage potential conflicts of interest and prevent anti-competitive behaviour."

• This article was amended on 10 April 2012 to include a statement from Virgin Health that procedures are in place to manage any potential conflicts of interest.