Khonglam, 67, passed away in a private hospital here on Tuesday evening after a brief illness.
Deputy Chief Ministers Rowell Lyngdoh and B M Lanong, Social Welfare Minister J A Lyngdoh and Parliamentary Secretary P W Khongjee besides his family members, friends and loved ones attended the funeral ceremony.
Governor R S Mooshahary, Chief Minister Mukul Sangma besides his other cabinet colleagues had visited Khonglam's residence to mourn the death of the former chief minister.
The state government had declared a three-day mourning since his death with the national flags flown at half-mast in all government buildings besides having declared a half-day holiday today.
A MBBS degree holder, Khonglam successfully contested assembly elections in 1983 from Sohra in East Khasi Hills district but lost in 1988. Five years later, he won again and remained the Sohra MLA till 2008.
With a distinction of being the first Independent MLA to occupy the CM