The news was conveyed by Habibie's son Thareq Kemal Habibie.
Families of the third president of Indonesia, including his two sons and grandchildren, have gathered at the hospital.
President Joko Widodo has arrived at the hospital to convey condolences to the family.
Habibie was born in Pare Pare, South Sulawesi on June 25, 1936 and led the country from May 1998 to October 1999.
Habibie's wife, Hasri Ainun Habibie, passed away in 2010 in a hospital in Germany.
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