A spokesman said that English Nature would have to accept that no other solution had been found to save the trees which line Queen Anne's Ride.
"We have been working closely with the Crown Estates and we gave them advice about the trees," he said.
"Of course we would have liked them to stay, but the estate office has to take other things than conservation into account, like aesthetics and safety. However, their decision is not ideal for us."
He said it would be possible for many of the trees, recognised as being of international conservation importance, to survive.
The renewed felling marks the second phase of work on Queen Anne's Ride, which was approved by the Duke of Edinburgh in 1992 to tidy up the park.
The much publicised decision provoked outrage in conservation circles and embarrassed the World Wide Fund for Nature, of which the prince is international president.
Despite claims that the project will restore and preserve a historic landscape feature, conservationists say the ancient oaks are home to many increasingly rare species of beetle and fungi.
The new trees that will replace them will take centuries to recreate the habitat the park offers the species.
The avenue was planted in 1720, but was hit by Dutch Elm disease and some trees were damaged in the storm of 1987.
In 1992, the Crown Estates announced that age and disease had withered the beauty of trees along the ride. They decided that in order to replace bare wood and gaps in the avenue they would have to fell all the trees along it and begin a process of replanting.
"Now we have to have the attitude that at least there will be something there in 300 years' time," said the English Nature spokesman.Reuse content