"I have serious reservations about this draft agreement" which leaves "deep-rooted problems" without solutions, he said in an interview with RFI radio.
Kafando said he was "not a part of the negotiations" mediated by the Economic Community of West African States (ECOWAS) that came up with the plan.
Burkina was plunged into turmoil on Wednesday when soldiers from the powerful presidential guard regiment loyal to ex-leader Blaise Compaore, who was ousted last year, detained Kafando and prime minister Isaac Zida, himself a former deputy commander of the unit.
Following the coup, Senegal's President Macky Sall, the rotating head of ECOWAS, undertook three days of mediation in a Ouagadougou hotel and on Sunday drafted a 12-point plan to end the crisis.
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The deal provides for presidential and parliamentary elections to be held by November 22 at the latest, and, crucially, would allow for pro-Compaore candidates to take part after they complained about being excluded from elections planned for October.
But civil society activists who played a major role in the uprising that toppled Compaore have condemned the proposals, with the main "Balai Citoyen" (Civic Broom) group branding the deal "shameful".
Kafando was also sceptical that any solution to the crisis would be achieved during an ECOWAS summit in Abuja on Tuesday.