Yunupingu, who is a former Australian of the Year, died overnight at his home in Yirrkala in Eastern Arnhem Land.
He had been ill with kidney disease for several years, the ABC says.
A relative of Yunupingu, who did not wish to be identified, confirmed his death on Sunday night at his home, near Nhulunbuy.
Yunupingu was a Yolngu man and a well-known identity in Arnhem Land.
He became the lead singer in Yothu Yindi, which was formed in 1986, a group which created a blend of rock and traditional Aboriginal music.
It became so popular Yunupingu had to give up his teaching job.
Yunupingu was the first Aboriginal person from Arnhem Land to gain a university degree, earning a Bachelor of Arts degree in education from Deakin University in 1988.
In 1989 he became assistant principal of the Yirrkala Community School. In 1990 he took over as principal of that school, becoming the first Aboriginal principal in Australia. He held this position until late 1991, leaving to pursue his career with Yothu Yindi.
He always said he believed that life should be balanced and in harmony and that his mother taught him important Aboriginal ideas about how to live with people and with nature.
His name, Yunupingu, means rock – rock that stands against time.
Yothu Yindi said in a statement on their website that the group was “mourning the death of its beloved lead singer.”
“He was an inspirational educator and leader: a huge force for good, happiness and change for his people and for Australia. We are incredibly proud of what we achieved together.
“His contribution as an educator, in the formation of the band, the Yothu Yindi Foundation, and its Garma Festival is unprecedented.
“He was such creative and unifying force, we hope his legacy goes on for ever. We will all miss him so much.”
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