Prince Charles, renowned for his aversion to “monstrous carbuncle” buildings, has spent £38m on an industrial depot in Milton Keynes as part of a £102m series of confidential property deals, The Independent can reveal. The purchase of the vast supermarket warehouse through his estate – one of the single largest acquisitions by the Duchy of Cornwall in its 670-year history – was completed 18 months ago but has been kept from being made public.

A recent judicial ruling declared the Duchy to be a “public body” potentially liable to freedom of information rules.

But Clarence House has repeatedly refused to disclose any details of the expensive acquisition due to what the Prince’s officials said was the Duchy’s “private” status.

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The Prince bought the sprawling grey warehouse complex in Milton Keynes from an Anglo-Indian property fund, The Independent has established. His tenants are Waitrose, who are using the depot as a lorry distribution hub. The deal offers a glimpse into the hard-nosed business ethos of the Duchy, established in the 14th century to provide an income for the Prince of Wales and his heirs, as well as the multiple layers of confidentiality and opaque procedure that govern the Prince’s commercial dealings.

Under an arrangement which is now being scrutinised by MPs, the Duchy is exempt from capital gains and corporation tax, saving it millions of pounds a year. Charles voluntarily pays income tax.

An investigation by The Independent has revealed that the Duchy, which is one of Britain’s largest private estates and owns more than 50,000 hectares of land, conducted property transactions worth at least £102m between 2009 and last December.

Any sale or purchase by the Prince worth more than £500,000 must be approved by the Treasury.

The Duchy’s holdings of land and property form the bulk of its assets, worth £693m, and stretch across 23 counties, including most of the Scilly Isles, Dartmoor Prison, the Oval cricket ground in central London, a Holiday Inn in Reading and the Prince’s private homes such as Highgrove. To this extensive list has now been added property title BM191066, otherwise known as the Waitrose distribution centre in Brinklow, Milton Keynes, whose new owners are listed by the Land Registry as “His Royal Highness Charles Philip Arthur George, Prince of Wales, Duke of Cornwall and Rothesay, Earl of Chester and Carrick, Baron of Renfrew, Lord of the Isles and Great Steward of Scotland”, and the Duchy. The sale price was £38,385,500.

Like all other significant Duchy transactions, the deal in November 2011 with Indian property fund Meghraj Properties had to be approved by the Lord Commissioners of the Treasury, an ancient post held by Government whips.

The depot, built in 1993 to withstand 20 million lorry journeys over its lifetime, sits awkwardly with the heir to the throne’s well-publicised love of traditional architecture along with his emphasis on rural life and environmental sustainability.

The purchase of the 396,000 sq ft warehouse is not the first link between Charles and the John Lewis Partnership supermarket. A previous deal between the Duchy and Waitrose in 2009 saw it take over the once-troubled Duchy Originals organic food brand, which now generates more than £1m a year for the prince’s charities.

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When The Independent yesterday approached Clarence House with evidence of the warehouse purchase, it insisted there was no connection with the Duchy Originals tie-up, adding it was a “coincidence” that Waitrose was the tenant of the industrial complex.

The revelations come at an uncomfortable time for the Duchy, which is facing a private members’ bill in the House of Lords demanding that its structure be radically overhauled and its surplus income – £18.3m last year – be distributed to Cornwall rather than to the heir to throne. The bill’s sponsor, Labour peer Lord Berkeley, says the Duchy is a “feudal anachronism”.

The day-to-day management of the Duchy, including investment decisions on commercial property such as the Waitrose warehouse purchase, is carried out by a professional managerial team. But it is widely known that Prince Charles takes a close personal interest in the running of the estate. In many ways, the estate, which transfers its handsome surplus every year to the heir to the throne to form the bulk of his income, is a paragon of success. Despite the global downturn, the Prince has defied the prevailing economic winds to grow the Duchy’s income every year since at least 2008 – to £26.5m last year. His estate’s total value has risen by 15 per cent to £764m.

Charles voluntarily pays income tax on the income he receives from the Duchy (last year he paid £4.5m to the tax man from incoming funds of £18.3m). He uses the money to fund himself and the Duchess of Cornwall, the Duke and Duchess of Cambridge, Prince Harry, a sizeable staff and his charitable activities.

But while the Duchy has been slickly managed, a growing number of critics say it has existed for too long in a constitutional no-man’s land where it discharges the duties of a public body, for example running the harbour authority on the Scilly Isles, and is subject to the financial scrutiny of Government whips, yet maintains it is a “private estate”. One benefit of this hybrid status is that the hereditary holding is exempt from both corporation and capital gains tax. The situation, which Clarence House insists is valid because the Duchy is “not a separate legal entity for tax purposes”, has led the powerful Commons public accounts committee, which is also investigating the tax affairs of Google and Starbucks, to demand answers from Treasury ministers as to whether the Prince’s exemptions are justified.

The Duchy is also fighting a separate attempt to force it to be more open about its workings. The Prince’s officials lost an important case before the Information Rights Tribunal, which after a three-year legal battle ruled that his estate was a “public authority” in performing its “primary function” to provide an income for the heir to the throne.

The landmark ruling could make the estate subject to the Freedom of Information Act. The Duchy is appealing. A spokeswoman said: “We do not agree that the Duchy performs functions of public administration. Hence we are appealing the ruling.”

Lord Berkeley, who lives in Cornwall, said there was a “conspiracy of silence” surrounding the status of the Duchy and it was time for a debate about its future: “The Duchy is a complete anachronism. It is feudal and I suspect many of those who work for it would say so if they felt able. It vacillates between being a private and a semi-public organisation according to its best advantage and yet there is no debate about how it should be best managed. It would seem to me that the Duchy would be a far better situation if it was turned into a public trust for the benefit of the people after which it is named.”

In a statement, a Duchy of Cornwall spokeswoman said: “The Duchy of Cornwall is a private estate, not a public body and is not funded by the taxpayer. The Prince of Wales chooses to use his private money from the estate to pay for his public duties, as well as those of the Duchess of Cornwall, the Duke and Duchess of Cambridge and Prince Harry.

“He also chooses to pay income tax on the income generated by The Duchy. The Duke of Cornwall manages the estate for present and future Dukes, and for the wider benefit of tenants, communities and the environment.”