Gluten-free prescriptions cost the NHS £27m last year, but that does not include handling and delivery charges, which are not recorded.
Gluten-free food products are available on the NHS to coeliac sufferers, a disease triggered by gluten intolerance.
However, it has been discovered that the NHS has been paying up to four times the original price for pizza bases.
An example from Rotherham showed that two gluten-free pizza bases purchased by the NHS originally cost £8.95. But once manufacturing, handling and delivery fees were added on, the bill had reached almost £34.
GP Dr Fayyaz Choudri told the BBC’s Newsnight that “We saw there were occasions where there was a bread loaf costing £2.50 and there was a handling fee of £32.”
The programme contacted a leading manufacturer of gluten-free food, which blamed wholesalers for the outlandish surcharges.
A gluten-free diet is essential for people afflicted with coeliac disease – without it, symptoms can include osteoporosis and bowel cancer.
Health secretary Andrew Lansley said prescriptions encouraged sufferers to stick to gluten-free diets.
But, he added, “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”.