Senior GPs are spending as little as one day a week seeing patients because they are too busy setting up new organisations as part of the coalition's health reforms, official NHS records reveal.

Family doctors are devoting as many as four days a week to setting up clinical commissioning groups (CCGs), the groups of family doctors that will become key NHS bodies from April 2013.

But it costs the NHS up to £123,900 a year to replace a GP with a locum. In one CCG area alone, 15 local doctors are each spending up to two days a week away from surgery, at a cost of almost £1m a year.

Doctors' leaders claim GPs' skills are going unused and that the costs involved show how vital NHS funds are being wasted on health secretary Andrew Lansley's radical restructuring of the NHS in England.

"It cannot make sense for experienced doctors to stop providing clinical expertise when the NHS is under such pressure. It's also incredibly bad timing as the NHS shouldn't be wasting precious resources on reorganising itself yet again," said Dr Laurence Buckman, chairman of the British Medical Association's GPs committee.

Freedom of information requests submitted to NHS primary care trusts (PCTs) by False Economy, the TUC-backed research group, show how many GPs are involved in setting up CCGs; how much time each is spending preparing the new set-up rather than treating patients; and the cost to the NHS of their being redirected into managerial tasks.

From April next year, CCGs will gradually gain control of £60bn of NHS funds as they replace PCTs in commissioning and paying for treatments on behalf of patients.

In Shropshire, Swindon and Camden, north London, doctors are spending four days a week organising the new CCG system. In 16 other CCG areas, at least one doctor spends at least three and a half days a week away from patients.

East and North Hertfordshire CCG is being created by one GP acting as its chair, working two days a week, and 14 GPas each spending an average of one and a half days on it. Each half-day session worked by each of the 15 GPs costs NHS Hertfordshire, the local PCT, £460. That means it is spending £973,360 a year on temporary replacements and "responsibility" payments to the 15 GPs – extra payments on top of their salaries to reflect their extra duties in relation to the CCGs.

The same PCT is also footing a £211,600 bill for the equivalent costs in the neighbouring, much smaller Herts Valley CCG, leaving NHS Hertfordshire spending a total of £1,184,960 on these start-up costs.

It is costing £654,500 to set up Oxfordshire CCG, covering for eight local doctors, including one acting as the CCG's chief executive, who is doing either seven or eight sessions a week with the new body, each lasting four hours and 10 minutes, at a cost of £15,400 per session per year.

Leicester City PCT is spending £545,564 a year covering for 10 doctors and three laypeople who are setting up the City CCG. Similarly, Brighton and Hove CCG is costing £455,450 a year to set up (with 15 doctors), while East Leicestershire and Rutland CCG is costing the local PCT some £434,182 (seven doctors and one layperson).

That CCG also contains the doctor who is costing the most to replace. The group's chair works seven sessions of three and three-quarter hours a week, with each of those sessions costing £17,700 a year, giving a total cost to the PCT for that GP's diversion into CCG duties of £123,900.

Five other individual doctors are each costing £100,000 to replace, including two in Bath and North East Somerset CCG – the accountable GP and the chair – who cost the NHS £100,100 each.

Labour warned that the disclosures underline the danger that patients could lose out in the new set-up because some GPs will spend part, much or all of their week helping to run the new CCGs. Andy Burnham, the shadow health secretary, said: "One of our major concerns about this bill is the damage it will do to the doctor-patient relationship.

It creates conflicts of interest and could undermine trust as GPs are forced to mix medicine and the money motive. It might also mean patients seeing less of the GPs they know and trust as they are taken away from the frontline.

"These plans are flawed on every level and represent a poor use of scarce NHS resources. It makes no sense to take GPs away from frontline patient care and pay [for] them twice in the process," he added.

Dr Clare Gerada, chair of the Royal College of GPs, said the disclosures underlined the case for expanding the number of GPs and the need to get CCGs to work together in federations to minimise the total amount of doctor time spent away from patients.

GPs helping set up CCGs was becoming "unsustainable" because most family doctors have "heaving workloads", Gerada said. Some were doing work in relation to CCGs in their lunch breaks and evening in order not to disrupt the service they provide to their patients, she added.

False Economy said the annual cost to the NHS of setting up CCGs was at least £20m, based on the replies it had from 106 of the estimated 230 CCGs that have emerged. But the true cost is probably nearer £40m when groups that had not replied or were not yet established are factored in, it believes.

Clifford Singer, False Economy's campaign director, said: "This isn't about greedy GPs – after all, GPs are overwhelmingly opposed to the bill that has created this situation. Instead, this is about chaotic reforms that are dragging GPs away from patients, and the inevitable financial costs of doing so.

"It is perfectly possible to increase doctors' involvement in NHS decision-making without creating these rigid, expensive and bureaucratic structures. The government's obsession with pursuing this bill has nothing to do with patient care or saving money and everything to do with privatisation and politics."

On Tuesday, both houses of parliament will discuss the health and social care bill, which is expected to finally become law next Tuesday.

Simon Burns, the NHS minister, defended GPs' involvement in the CCGs. "Putting GPs in leadership positions in the NHS will mean they can improve services for their entire local population. Patients want doctors to make decisions about their care, not managers, and that is what our reforms will deliver.between now and 2015 because we are removing large swaths of bureaucracy. This money will be reinvested in the NHS," he said.