The project dooms 239 limes, oaks and chestnuts - some of them up to 270 years old and many providing homes for rare species of beetle and fungi.
However, officials at English Nature, the Government's conservation body, hold conflicting views on the plans.
One body of opinion says that the Crown Estate, which runs the 15,000-acre park for the sovereign as part of Civil List arrangements, has full official approval for the felling scheme after lengthy negotiations. Another says that some insiders at English Nature are angry, particularly at the loss of 35 ancient oaks which are of greatest scientific interest. One official said: 'I am deeply alarmed that they are cutting down these trees unnecessarily.'
So sensitive is the issue that few will discuss it on the record, despite 18 months of talks between the Crown Estate and English Nature. One senior source at the conservation body said that he would have to report my call to senior colleagues, adding that he was 'sorry for acting like MI6'.
Another agreed to speak, but then faxed full details of our conversation to Roland Wiseman, the Crown Estate chief at the park. The fax arrived while I was interviewing Mr Wiseman.
Such touchiness can mean only one thing: the Royals are deeply interested in the project. The Duke holds the title of head ranger at Windsor and, according to Mr Wiseman, he is 'totally in favour' of the proposed felling.
This centres on a grassy avenue called Queen Anne's Ride which spears straight into the heart of the estate, carrying twin lines of lime trees with some chestnuts and occasional oaks, many of which are part of the original 1720 planting.
Windsor is famous for its ancient oaks. It has about 6,000, providing perfect habitats for increasingly rare species of beetle and fungi which feed on their rotting limbs. Take away the old oaks and the beetles and fungi - collectively known as saproxylics - die.
The problem with Queen Anne's Ride, according to the Crown Estate, is that age and disease has withered its beauty, creating gaps and forming patches of unsightly bare limbs. Almost-complete felling, then replanting with 1,000 tiny oak saplings, is the only way to restore the original loveliness.
Some people disagree. One suggestion is that the older trees should be left to stand while new trees go in alongside. Professor John Owen, a distinguished amateur entomologist who has made a study of Windsor wildlife, said: 'I believe that the removal of any oak trees of that vintage is quite undesirable. The argument that there are plenty of other old trees and so we can cut down these really doesn't hold.'
The project is due to take up to four years to complete, but its effect may not be noticed by the public for some time because access to the first third of the Ride - where work will begin - is restricted.
Mr Wiseman denied that the scheme was intended to mark the 40th anniversary of the Queen's accession to the throne.
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