A leading scientist has revealed how he nearly lost his job after Prince Charles's most senior aide made an official complaint about him. Professor Edzard Ernst was accused of breach of confidence after criticising a report commissioned by the Prince.

The revelation will reignite the controversy over whether Prince Charles is interfering in government policy. A Channel 4 Dispatches programme will tomorrow examine a range of areas where he is said to have 'meddled' in affairs of state.

Clarence House has issued a 17-page denial of the claims made in the programme, which says that Charles uses his influence both publicly and privately across a range of issues, such as organic farming, planning and medicine.

The Ernst controversy began in July 2005 when, as professor of complementary medicine at Exeter University, he was asked to look at a draft report written by economist Christopher Smallwood, who was investigating whether alternative remedies such as acupuncture were cost-effective and should be funded more widely on the NHS.

Ernst signed a confidentiality agreement for an interview he gave to the report team, but became worried by the report itself. A draft he saw claimed that the NHS could save between £500m and £3.5bn if there was a switch to alternative therapies. He was then called by a newspaper, which had a copy of the draft, and described the initial findings as 'outrageous and deeply flawed'. He added: 'It is based on such poor science, it's just hair-raising. The Prince ... also seems to have overstepped his constitutional role.'

Shortly afterwards the vice-chancellor of Exeter, Professor Steve Smith, received a letter from Sir Michael Peat, Prince Charles's private secretary, alleging that Ernst had committed a serious breach of confidentiality. The action led to him facing a year of disciplinary hearings and investigations, which could have resulted in his dismissal. Last December he was cleared of wrongdoing.

The letter is dated 22 September, 2005, and is written on headed notepaper from Clarence House and signed by Sir Michael Peat, who states that he is writing 'both as the Prince of Wales's Principal Private Secretary and as acting chairman of His Royal Highness's Foundation for Integrated Health'.

He writes: 'There has been a breach of confidence by Professor Edzard Ernst in respect of a draft report on the efficacy of certain complementary therapies sent to him by Mr Christopher Smallwood. The report was commissioned by the Prince of Wales.' Peat commented in a written statement to The Observer: 'This letter was not prompted by His Royal Highness and he was not even aware that it had been written. The letter was sent at the express request of the trustees for the Foundation for Integrated Health, and it was made clear in the letter that I was writing as the foundation's chairman as well as the Prince's Principal Private Secretary.

A spokesman for Exeter said: 'The Channel 4 programme will also highlight the fact that there have been several meetings between the Prince, his staff and members of the Medicines and Healthcare Products Regulatory Agency (MHRA), which regulates medicines and also looks at treatments such as homeopathy and herbal remedies.'