A Reuters journalist in Tinzaouaten on the border with Algeria witnessed the strike on the town, which is under the control of a rebel coalition known as the Permanent Strategic Framework for the Defense of the People of Azawad (CSP-DPA).
Tuareg factions had been meeting in Tinzaouaten this week to form a unified political and military structure.
"Several CSP cadres were killed, including the notorious Fahad Ag Almahmoud," Chodi Ag, a mission manager at Mali's communications ministry, said in a post on Facebook.
Separatist groups from northern Mali, largely dominated by ethnic Tuaregs, launched a rebellion against the government in 2012, which was later subsumed into an insurgency by Islamist groups linked to al Qaeda and the Islamic State.
A 2015 peace agreement between the government and rebels collapsed in July this year and triggered renewed fighting, including a fierce battle around Tinzaouaten that killed dozens of Malian soldiers and Russian Wagner mercenaries.
Almahmoud was a key member of the CSP alliance. He ensured coordination between its factions and represented them in discussions with authorities about the peace agreement.
A military source who did not wish to be identified said strikes on Tinzaouaten had killed Almahmoud and other "terrorist leaders."
The army has not officially commented on the attack.
Multiple drone strikes since the July conflict have killed dozens of civilians in Tinzaouaten, including children, doctors and residents.
