Data obtained by GP shows 55 per cent of UK primary care organisations (PCOs) do not follow NICE or SIGN guidance on bariatric surgery.
This has blocked thousands of patients from treatment to which they are entitled under the NHS Constitution.
Experts believe GP consortia could improve access to obesity surgery by adhering to NICE advice. But GPC leaders warned that a lack of resources meant consortia would be unable to afford this, leaving them open to legal challenges from patients.
Both NICE and SIGN recommend that patients with a BMI of 40, or 35 with a co-morbidity, undergo bariatric surgery as a last resort after intensive lifestyle interventions. NICE estimates 240,000 patients could benefit.
However, data obtained by GP from 118 PCOs under Freedom of Information Act rules show many have rationed the procedure, often by raising BMI thresholds to 50 or 60.
National Association of Primary Care president Dr James Kingsland said variations in bariatric surgery should be reduced by GP commissioning. 'I would like to think there will be a lot more evidence-based medicine,' he said.
Dr David Haslam, director of the National Obesity Forum and member of group Experts in Severe and Complex Obesity (ESCO), said: 'The only surprising thing is that so many (PCOs) claim to be sticking to NICE guidance.'
He hoped GP commissioners would recognise the evidence of its cost effectiveness.
Data from PCOs showed large regional variation in the number of weight loss procedures. NHS Stockton-on-Tees carried out the most procedures on a population basis in 2009/10, with 5.9 operations per 10,000 people. NHS Rotherham funded just one operation among its 244,000 population.
One third of PCOs do not provide specialist obesity services essential to preand post-operative care. Instead, patients are referred to other PCOs. Some said they cannot afford obesity surgery for all eligible patients.
GPC deputy chairman Dr Richard Vautrey said: 'I don't expect the situation to change as the reason these restrictions are in place is lack of resources, and that will only get worse.'
If this occurs under GP commissioning, cash-strapped consortia could be forced to tell patients that they cannot afford bariatric surgery even though their GP recommends it.
The NHS Constitution entitles patients to treatment recommended by their clinician and NICE. In August, a patient took legal action against NHS Berkshire East after it said her BMI, which was within NICE guidance criteria, was too low for bariatric surgery.
Dr Vautrey said not following NICE guidance could have legal repercussions for GP commissioning groups. 'It will leave consortia vulnerable to legal challenge in the same way as PCTs,' he said.
The Medical Defence Union said it was too early to know if patients could sue individual GPs on this basis.
A DoH spokeswoman said: 'Whether to prescribe drugs or recommend surgery is rightly a clinical decision. It is up to individual trusts to commission a range of services to meet their local community's needs.'
Source: GP investigation/Royal College of Surgeons.