The move to create "human exclusion zones" was announced by Domestic Operations Chief Lieutenant Colonel Yves Didier Bamouini.
"The decision was taken at a defence council convened on Monday by junta leader Lieutenant Colonel Paul-Henri Sandaogo Damiba to discuss the country's "worrying security situation".
"The council decided to create two zones of military interest in the East and (northern) Sahel regions," Bamouni, said.
The lieutenant said the aim was to make it easier to combat "the terrorist hydra."
The areas are in the northern Soum province bordering Mali, and the protected natural reserves between Pama and the "W" National Park in the east.
All human activity and human presence will be banned in the zones. Anyone who ventures into them risks exposing themselves "to the military operations that will be conducted there shortly", Bamouni said.
The decision comes 10 days after 86 civilians were massacred in an attack blamed on jihadists on the northern border village of Seytenga.
It was the second worst attack since 2015, when violence attributed to fighters linked to Al-Qaeda and the Islamic State group began.
Thousands have since died and nearly two million people have fled their homes.
The new government led by Damiba, who overthrew elected president Roch Marc Christian Kabore in January, vowed to restore security, blaming Kabore of not doing enough to repel armed jihadists groups.