Draft guidance for the website NHS Choices warning that there is no evidence that homeopathy works was suppressed by officials following lobbying by a charity set up by the Prince of Wales.

Homeopathy, which involves the use of remedies so heavily diluted with water that they no longer contain any active substance, is "rubbish", said chief medical officer Sally Davies in January to the House of Commons science and technology committee. She added that she was "perpetually surprised" that homeopathy was available in some places on the NHS.

But the government's NHS Choices website, which is intended to offer evidence-based information and advice to the public on treatments, does not reflect her view. A draft page that spelled out the scientific implausibility of homeopathic remedies was neutered by Department of Health officials. It is now uncritical, with just links to reports on the lack of evidence.

Lobbying by opponents, and the response from DH officials who did not want to take on Prince Charles's now defunct Foundation for Integrated Medicine and other supporters of homeopathy, is revealed in correspondence from the department discussing the new guidance. It was released under the Freedom of Information Act to Prof David Colquhoun of University College London, a Fellow of the Royal Society and prominent science blogger.

There is no evidence that Prince Charles was involved personally in the lobbying.

The editor of the draft advice, David Mattin – who has now left NHS Choices – said in a statement to Colquhoun, published on his blog, that the DH had failed patients. "In causing NHS Choices to publish content that is less than completely frank about the evidence on homeopathy, the DH have compromised the editorial standards of a website that they themselves established and that they fund. They have sold out the NHS Choices editorial team who work tirelessly to fulfil their remit. And, most seriously, they have failed the general public, by putting special interests, politics and the path of least resistance (as they saw it) before the truth about health and healthcare."

NHS Choices has offered information on homeopathy since at least 2007, but it has been heavily criticised for its failure to state that there is no proof that homeopathy has anything other than a placebo effect on patients.

The page was taken down early in 2011, pending what a statement on the site said would be "a review by the Department of Health policy team responsible for complementary and alternative medicines". But critics were disappointed by the page that went up in October 2012, which still does not raise any issues about effectiveness.

What had been happening behind the scenes in the couple of years before the disappearance of the page and during its absence is revealed in the correspondence between NHS Choices, department officials and the foundation.

Mattin's original draft said: "There is no good quality clinical evidence to show that homeopathy is more successful than placebo in the treatment of any condition … Furthermore, if the principles of homeopathy were true it would violate all the existing theories of science that we make use of today; not just our theory of medicine, but also chemistry, biology and physics."

But the homeopathy lobby was in close contact with the department. In December 2009, an official from the department wrote to NHS Choices asking to see "the articles you're writing" and announcing that he had called "an exploratory meeting with the Prince's Foundation for Integrated Health and the Complementary and Natural Healthcare Council … so that we could start to piece this particular jigsaw together."

On 29 December, a letter was sent from the foundation to the department expressing strong feelings about a draft document. "It was just a bit horrifying as it was not only anti-complementary medicine and patients who might use it but clearly drawn up by someone who had no knowledge of this field and was largely factually incorrect," said the letter.

In January, further emails from the foundation strongly opposed the involvement of the Exeter-based professor of complementary medicine, Edzard Ernst – now retired and a strong critic of homeopathy – as an adviser.

The documents reveal subsequent changes to Mattin's draft by DH officials. The draft stated: "A House of Commons science and technology report said that homeopathic remedies perform no better than placebos and that the principles on which homeopathy is based are 'scientifically implausible'."

That critique disappeared. A comment in the margin, apparently from somebody in the department, says: "Can we remove this statement? This report is really quite contentious and we may well be subject to quite a lot of challenge from the homeopathic community if published."

A further intervention by the DH also removed the statement that "a 2010 science and technology committee report said that scientific tests had shown that homeopathic treatments don't work."

Mattin says officials were more worried about potential political fallout from homeopathy supporters than about publishing evidence-based information. He says his draft was delayed and then suppressed.

"My strong impression was of DH civil servants who lacked the courage and, frankly, the energy to stand up to the criticism from special interest groups that they anticipated would arise because of the article; and that indeed did arise when a draft of the article and other draft content on complementary and alternative medicines fell into the hands of the Prince's Foundation and other [complementary and alternative medicine] groups."

The department did not respond to a request to comment. The Prince's Foundation for Integrated Health was closed in 2010 following allegations of fraud and money-laundering that led to the conviction of a charity official for stealing more than £250,000.