The John Muir Trust, which campaigns for the protection of wild lands, has been criticised for its proposals on the Quinag Estate in Assynt, Sutherland, which it says are necessary to protect woodland habitats.
Landowners in the area – who share the deer population – have been particularly critical, with objections to such a big increase on the recommended cull levels.
A statement from the trust said: "Some people claim we want to kill all deer, that we favour trees over people, that our deer management on Quinag threatens tourism.
"Heavy browsing by deer prevents trees from regenerating. Scotland already has some of the lowest tree cover in Europe – we can't afford to lose more, especially of the native variety."
Suggestions that better fencing would protect the tree population have been rejected by trust. It added: "Deer fencing treats the symptoms but not the cause. Fences are expensive and a blot on our scenic landscapes. Crucially, they do not prevent deer culling."
The trust said the key is to get deer to a sustainable number "so that we can have deer and trees living together without fences.
"This isn't radical. It's the way it was for thousands of years and it's the way it is today in many other countries in the world."
In response to neighbouring landowners, the trust said it was more important for many estates to have high deer numbers available for their shooting clients.
It added: "The number required for this purpose is often up for debate – how many is enough? Can there ever be enough for a client who has paid a lot of money and wants a stag on the one day they have paid to go stalking?"
The trust estimates 296 stags are on Quinag and says it would not cull the full 100 if the impact on trees was reduced.
Jim Payne, owner of the adjacent Ardvar Estate, claimed the figure was excessive.
He said the Ardvar and the 9140-acre Quinag Estate shared a common deer herd which, until May this year, had been managed by Ardvar.
He said: "The average number of stags culled in the last three years has been 25 on the two estates."
He said Scottish Natural Heritage had proposed a cull this year of 20 stags off Ardvar and 25 stags off Quinag.
The Assynt Crofters' Trust which acquired the 21,000 acres North Assynt Estate in a historic buy-out 20 years ago – paving the way for the likes of Eigg, Knoydart and Gigha – has also raised concerns about the cull.