An aide in Prince Charles's campaign for wider use of complementary medicine in the NHS was arrested at dawn today on suspicion of fraud and money-laundering at the prince's health charity.

A 49-year old man, understood to be a former senior official at the Prince's Foundation for Integrated Health, was taken into custody at a police station in north London. He was arrested alongside a 54-year-old woman, who was being held at the same address.

The arrests follow a police investigation into £300,000 unaccounted for in the books of the charity, of which the Prince is president.

The foundation promotes homeopathy, herbal remedies and other complementary medicines, in line with the prince's advocacy of their wholesale application in the public health sector.

"Officers from the Metropolitan police service's economic and specialist crime command arrested two people this morning on suspicion of fraud and money-laundering at an address in north-west London," said a spokeswoman for Scotland Yard. "They were arrested at around 7am and taken to a north London police station, where they remain in custody. The arrests are in relation to a complaint alleging fraud by the foundation for integrated health."

Prince Charles established the charity in 1993 to explore "how safe, proven complementary therapies can work in conjunction with mainstream medicine". But since then his ventures in complementary medicine have been attacked in some quarters as unscientific.

Edzard Ernst, professor of complementary medicine at Exeter University, last year described a detox tincture made by the prince's Duchy Originals company as "outright quackery". Profits from Duchy Originals have helped to fund the foundation. It has also received more than £1m in public funds, mainly from the Department of Health since its launch in 1993, and almost £3m from the Prince's Charities Foundation, which handles his personal giving.

Clarence House declined to comment on the arrests, saying: "It is a matter for the police." A spokeswoman for the foundation said: "We can't comment on this matter at this time."

The charity has faced controversy in recent months.

Regulators have been asked to investigate a complaint the prince broke charity rules by using it as a mouthpiece for his opinions on healthcare; they are also examining whether its staff pursued a public "vendetta" against Ernst.

The prince's private secretary, Sir Michael Peat, filed an official complaint to Exeter University about the professor after he publicly attacked the foundation's draft guide to complementary medicines as "outrageous and deeply flawed".

In February, the Commons science and technology select committee concluded that there is no evidence that homeopathy has anything other than a placebo effect, and said manufacturers should no longer be allowed to make therapeutic claims.

The foundation has attracted donations from the alternative health industry, including Solgar Vitamin and Herb, and A Nelson and Co, a UK manufacturer of complementary medicines.

The foundation's accounts for 2008 are overdue at Companies House and it risks a £1,500 fine.