Almadi Ag Lengach -- the military chief of the Imghad and Allies Tuareg Self-Defence Group known by the French acronym GATIA -- was slain at home in Menaka, one of its fighters told AFP.
"(Ag Lengach) was killed at home by armed men who then ran off," said GATIA member Mohamed Ag Ouleg.
A Malian security source said the assassins scaled the walls of Ag Lengach's house to evade his security detail before killing him.
The GATIA, which supports the central government in Bamako, signed a 2015 peace deal with state authorities and members of the country's former rebel alliance that is aimed at quelling uprisings in the north.
A 2012 rebellion by the Tuareg-led rebels was hijacked by jihadists who then seized control of key northern cities, triggering an international military intervention the following year.
Since the peace deal aimed at ending the conflict, the GATIA has been accused of multiple ceasefire violations, and in September last year US ambassador to Mali Paul Folmsbee told the government it should "sever all ties" with the group.
Ag Lengach's murder comes as the country struggles to implement key elements of the peace deal including temporary regional bodies charged with organising elections when security can be assured for voters.
The interim authorities, as they are known, were put into place on March 2 in Menaka but remain absent in the restive city of Timbuktu, where armed groups have also clashed repeatedly.
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