During his time as president, Dr Habibie apologised for past human rights abuses and ordered the release of political prisoners, dismantled restrictions on the press and reformed politics to allow for free elections.

Following the ouster of dictator Suharto and responding to international criticism of Indonesia's occupation of Portugal's former colony of East Timor, Dr Habibie surprised Indonesians by announcing in January 1999 a plan to hold a referendum under UN supervision on self- determination, offering a choice between special autonomy and independence.

But East Timorese voted overwhelmingly to split from Indonesia.

"Not only Indonesian people lost him, but we also lost him," East Timor Prime Minister Taur Matan Ruak wrote on Twitter. "He gave us two options and now East Timor is a free and independent nation. Farewell Mr. Habibie."

Loading

President Joko Widodo led Thursday's ceremony, attended by more than 700 politicians, government officials, foreign diplomats and public figures, including former presidents Megawati Soekarnoputri and Susilo Bambang Yudhoyono.

"He is a true statesman, an inspirator, a scientist who believes that without love intelligence is dangerous," Widodo said in a farewell speech. "He is truly a role model for all of the nation's children ... surely Indonesia has lost one of its best sons."

Islamic prayers were said, and as his body was lowered, mourners tossed flower petals into his grave, alongside that of his wife of 48 years, Hasri Ainun Habibie, a medical doctor who died in 2010.

The government has declared three days of national mourning.

Foreign leaders and diplomats offered their condolences, including Australian Prime Minister Scott Morrison.

On Thursday, Mr Morrison said on Twitter:  "He led the Republic of Indonesia at a time of massive change. His courage and vision during the period of reformation were appreciated in Australia."

"We will always remember your message: don't get into too many discussions, don't be whiny, but immerse yourself into the process of adding value consistently and Indonesia surely will be prominent in Southeast Asia and the world," Widodo said in his farewell speech.

Dr Habibie is survived by two sons.