At least 150 panes of glass were also smashed in the garden’s hot houses during the storm, which saw wind speeds reach 100mph.
Mr Milne said staff had since wrapped many of the tropical plants in material in a bid to protect them from Scotland’s wintry weather while the windows are being fixed.
The Himalayan cedar’s wood is too brittle to make furniture, but staff hope they can find a use for it. They have not yet decided whether the stump of the tree will be left or uprooted.
The tree is currently cordoned off to the public for safety reasons but can be clearly seen from a path in the historic garden, which has now reopened to the public.
Mr Milne said they had started fundraising to cover the cost of the damage which runs into hundreds of thousands of pounds across its four sites across Scotland: Edinburgh, Benmore, Dawyck, and Logan.
The Royal Botanic Garden Edinburgh, external is home to one of the largest and richest plant collections in the world.
It was closed on Friday during the storm so nobody was injured by the falling trees.
The Himalayan cedar is regarded as a holy tree in its native country and its Sanskrit name means “wood of the gods”.
