Two prescription gluten-free pizza bases can cost the NHS as much as £34, BBC Newsnight has learned.
The NHS spent £27m on gluten-free prescriptions in 2011, but handling and delivery charges, which can quadruple the cost, are not recorded.
Coeliac disease sufferers can develop serious illnesses if they eat gluten.
Health Secretary Andrew Lansley said prescriptions encouraged sufferers to stick to gluten-free diets but that the area was "under ongoing review".
"The aim of providing gluten-free food products on NHS prescription is to encourage patients with coeliac disease to stick to a gluten-free, nutritious diet so they do not go on to develop more serious illnesses, which can affect their quality of life as well as being much more costly for the NHS," he said in a statement.
"However, we keep this area of prescribing under ongoing review and are currently considering how we might get better value from the prescribing of gluten-free products whilst ensuring patients continue to get the products they need."
Gluten-free bread, cake mixes and bourbon biscuits are also available to people with coeliac disease, an auto-immune disease, which is triggered by eating gluten, which is found in wheat, barley and rye.
In an example from Rotherham, it was discovered that the NHS had been paying four times the original price for pizza bases.
The two pizza bases originally cost £8.95. But by the time manufacturing, handling and delivery fees were added on, the bill for the NHS had been driven up to nearly £34.00.
Another example comes from Dr Fayyaz Choudri, a GP who was responsible for overhauling gluten-free prescriptions in Allerdale, Cumbria.
"We saw there were occasions where there was a bread loaf costing £2.50 and there was a handling fee of £32.00," he says.
Dr Choudri has coeliac disease himself and knows the importance of a gluten-free diet.
Without it, symptoms can range from digestive disorders to very serious illnesses including osteoporosis and bowel cancer.
Geoff Martin is one of a growing number of people in the UK diagnosed with the disease.
"This is a lifetime complaint. When you've got it there is no cure for it," he says.
The condition is triggered by an intolerance to gluten, a protein found in wheat, barley and rye - and therefore a common ingredient in many processed foods.
"The only solution to it," Geoff continues, "is eating food that is gluten free."
Living as he does in rural Oxfordshire, this is a problem. In order to guarantee a varied and balanced diet, Geoff relies on his prescriptions for gluten-free food.
Geoff's NHS trust is one of many now reviewing its policy on gluten-free food.
With an estimated one in 100 people affected by gluten intolerance, campaigners want the NHS to continue providing staple foods like bread and pasta.
These are increasingly available in shops, along with a wide range of gluten-free products. But they are often much more expensive than regular foods.
Coeliac UK, which represents sufferers, worries that the hidden costs of prescriptions (which patients pay for, unless they have other conditions which qualify them for free scripts) is giving the whole system a bad name.
Newsnight contacted one of the leading manufacturers of gluten-free food, Juvela. They blamed wholesalers for adding "extra charges, sometimes adding a £20 handling charge to a £3 loaf".
This is questioned by the British Association of Pharmaceutical Wholesalers, which represents some of the biggest companies.
They told us they would be "keen to investigate any relevant cases of alleged poor standards or distribution practice."
To try to safeguard prescriptions, Coeliac UK has drawn up guidelines for NHS trusts on what sort of items should be prescribed - recommending that biscuits and cake mixes should only be given in "exceptional circumstances."
But Newsnight has contacted five trusts which say they have not passed on the guidelines, and that cakes and biscuits are still available on prescription.
With NHS budgets under relentless pressure, these are increasingly being seen as rations the NHS cannot afford.
Watch Liz MacKean's full report on gluten-free prescriptions on Thursday 24 May at 22:30 BST on BBC Two, then afterwards on the BBC iPlayer and Newsnight website.