Khandekar had also served as the personal secretary to former Maharashtra Chief Minister Y B Chavan.
Sources said that he died late Tuesday night in his hometown Nagpur in Maharashtra.
Khandekar was invited by Narasimha Rao in 1985 to oversee the work of Ramtek in his then-constituency Nagpur.
When Rao became Prime Minister in 1991, Khandekar served as his Officer on Special Duty (OSD). He was considered Rao’s confidant and worked with Rao till his death.
Khandekar often wrote articles in various Marathi newspapers.
He is survived by his son, daughter-in-law and two grandchildren.