The wild elephants damaged the garden located at the Balayatrie Estate bungalow at Boikeri on Madikeri-Mysore Road.
Khan, once an associate of former chief minister R. Gundu Rao, was a Rajya Sabha member and close to the late Sanjay Gandhi.
The former Rajya Sabha member was known for his love for gardens and won accolades for maintaining the best garden in Delhi in his MP bungalow.
Back in Kodagu after his controversial political innings, Khan had been nurturing his garden and has been holding annual private flower show since 1998.
Khan has criticised the Karnataka government for not taking steps to tackle the jumbo menace in Kodagu.