At least 10 people have been killed and more than 100 injured in protests sparked by the coup.
A dozen soldiers were killed in northern Burkina Faso when unidentified gunmen attacked a military post near the border with Mali, President Roch Marc Christian Kabore said while calling the assailants “forces of evil”.
He said those killed were members of the army’s special anti-terrorist group.
“This attack demonstrates that the fight against terrorism will be without respite and also underscores the necessary decisions that must be taken to give confidence and vitality to our army,” Kabore said.
Two more men were missing after about 40 armed men, riding pick-up trucks and motorbikes, attacked the Nassoumbou base on Friday morning, Mohamed Dah, commissioner of Soum province, told AFP news agency.
“They [the attackers] were heavily armed with Kalashnikovs and rocket-launchers,” Dah said. “They opened fire at the depots, the tents and set fire to some of the vehicles.”
There was no immediate claim of responsibility.
The army said in a statement it had sent reinforcements.
Troops at the Nassoumbou base are part of a 600-strong counterterrorism battalion that was deployed in January 2013 when France sent in troops during the unrest in northern Mali.
Attacks in Burkina Faso were rare before a major strike by al-Qaeda-linked fighters on a hotel in the capital Ouagadougou killed 29 people in January.
In September, a newly formed armed group, led by a fighter formerly loyal to Algeria’s Mokhtar Belmokhtar, claimed to have attacked a military position in Burkina Faso.
And unidentified gunmen also killed three soldiers and two civilians in October.