The head of the Royal Botanic Gardens says he is sad, but determined to take positives from the death of the 400-year-old Separation Tree, one of Melbourne's landmarks.

On Monday, for safety reasons, arborists will begin lopping branches and the trunk of the towering, heritage-listed river red gum, which vandals killed by ringbarking.

The once majestic tree was one of the few left in the gardens that pre-dated European colonisation.

It is believed to date from the 17th century when Indigenous tribes met by the Yarra River.