Homeopathy through the NHS costs between £4m and £12m a year and is a waste of taxpayers' money, according to retiring scientific adviser to the government Professor Sir John Beddington.
"Homeopathy... has no underpinning of scientific basis," he said. "In fact all of the science points to the fact that it is not at all sensible. The clear evidence is saying this is wrong, but homeopathy is still used on the NHS."
The Prince of Wales is among the advocates of homoeopathy and Jeremy Hunt, the health secretary is also known to be a supporter.
Sir John said the subject of homoeopathy on the NHS was the only occasion during his five years as chief scientific adviser that his views had been "fundamentally ignored" by the Government.
In 2010, the Parliamentary Science and Technology Committee said that government should "stop allowing the funding of homeopathy on the NHS".
The British Medical Association said homeopathy was "witchcraft", adding: "At a time when the NHS is struggling for cash we should be focusing on treatments that have proven benefit. If people wish to pay for homeopathy that's their choice but it shouldn't be paid for on the NHS until there is evidence that it works."
The Department of Health said it did not maintain a position on any particular complementary or alternative therapy, including homeopathy.
"It is the responsibility of local NHS organisations to make decisions on the commissioning and funding of any health care treatments for NHS patients, such as homeopathy," the DH said. "This should take account of issues to do with safety, clinical evidence and cost-effectiveness and the availability of suitably qualified and regulated practitioners."