Interim President Traore said Friday "We are confronted with a security and humanitarian crisis without precedent."
"Our aims are none other than the reconquest of territory occupied by these hordes of terrorists," he added. "Burkina's existence is in danger."
Traore pledged support for a transition leading to elections in July 2024 as he took the oath of office in the capital Ouagadougou under tight security.
Traore, 34, led disgruntled junior officers last month in the second coup in eight months to hit the west African country, toppling Lieutenant-Colonel Paul-Henri Sandaogo Damiba.
The motive -- as in January -- was anger at failures to stem a seven-year jihadist insurgency that has claimed thousands of lives and driven nearly two million people from their homes.
Damiba himself had seized power only in January, forcing out Burkina's last elected president, Roch Marc Christian Kabore.