"M5-RFP distances itself from the resulting document which does not reflect the views and decisions of the Malian people", said the coalition in a statement.
A meeting is planned on Tuesday in Accra between ECOWAS and Mali.Regional powers anxious that political instability will undermine a years-long fight against armed groups across West Africa, have pushed for a swift transition back to civilian rule.
Fresh crisis looms in Mali as popular opposition movement has rejected a charter for a transition government backed by the ruling army officers who ousted President Ibrahim Boubacar Keita.
One of the discrepancies between the negotiations and charter was the majority pressure for a civilian interim president.
It also said that the discussions had taken place against a backdrop of "intimidation, antidemocratic and unfair practices worthy of another era". Leaders of Mali's military junta who deposed the West African country's president last month are meeting with political parties and civil society groups to outline a transition to a civilian government and, ultimately, elections.
But M5-RFP and West Africa regional bloc ECOWAS insist only a civilian can take charge of the transition. ECOWAS has already stopped financial transfers into the country and has closed its borders with Mali.
The military junta backed a charter for an 18-month transition government on Saturday, after a three-day forum with political parties and civil-society representatives.
Global powers have been concerned that ongoing instability will undermine the fight against Islamist militants in West Africa's Sahel region.