Mali's junta leader Assimi Goita (L) and Niger's General Abdourahamane Tiani (R).
The two rebel groups are fighting the respective juntas in Bamako and Niamey which seized power in recent coups.
Mali and Niger, along with military-led Burkina Faso, have broken away from former colonial power France and regional bloc ECOWAS, turning politically and militarily towards Russia.
"A delegation from the CSP led by its president Alghabass Ag Intalla met a mission from Niger's FPL led by commander-in-chief Barka Taher Hamit from August 25 to 29 in Tinzaouatene", a town in northern Mali, said CSP spokesman Mohamed Elmaouloud Ramadan.
The CSP is a coalition of mainly Tuareg-led armed separatist groups.
Tinzaouatene, located near the Algerian border, was the site of a major late July battle in which separatists and jihadists claimed to have inflicted a serious defeat on the Malian army and the Russian paramilitary group Wagner.
On August 25, drone strikes on the town killed around 20 civilians, including several children, according to the separatists, a local elected representative and an official from a local NGO.
The Malian army said it had destroyed "terrorist targets" and killed "around 20 armed individuals" during the operation.
Speaking of the late August meeting, CSP spokesman Ramadan said "the exchanges were fruitful, covered subjects of common interest and helped to strengthen our relations".
"At a time when the juntas have decided to carry out ethnic cleansing, we must organize ourselves to defend our territories and our people", he added.
The FPL, which is fighting for the release of Niger's ousted president Mohamed Bazoum, confirmed the meeting on its social media.
"Discussions focused in particular on the need to sign a mutual assistance pact in the event of aggression by the states of the AES", a new confederation made up of Mali, Burkina Faso and Niger, the FPL said on its Facebook page.
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