"Terrorism is expanding," Chergui told journalists on the sidelines of an AU summit in Addis Ababa, pointing in particular to countries on the Sahara's southern rim.
"There are increasing numbers of terrorist movements, who attack civilian populations and institutions in these countries."
"Almost on a daily basis, Burkina Faso now is facing criminal and terrorist attacks," he said.
Chergui said the combination of extremist attacks, inter-ethnic conflict and clashes between pastoral and agricultural communities was leading to an "unprecedented high level of violence."
He said that AU member states had agreed to address the scourge of extremism in a more comprehensive manner.
This meant not only through "military and security responses, but also other means in terms of governance, in making sure that no one is left on the road in terms of development, in terms of political engagement, in terms of justice," he said.
He highlighted youth unemployment as a key challenge.
His comments echoed those of Egyptian President Abdel Fattah al-Sisi, who took over as AU chair on Sunday with a call to tackle the root causes of extremism.
Chergui expressed disappointment in difficulties faced to finance the G5 Sahel force, a French-backed 5,000-man joint mission among the five nations on the front line: Burkina Faso, Mali, Mauritania, Niger and Chad.
The Islamist revolt in the Sahel took off after chaos engulfed Libya in 2011. Jihadist attacks erupted in northern Mali as Boko Haram arose in northern Nigeria.
The French army largely flushed jihadists from Mali, but they have gained ground in neighbouring Burkina Faso and Niger, while Chad is battling unrest on its borders.
Lack of funding and training, as well as poor equipment, have hobbled the G5 Sahel initiative.
"The troops are ready, but there is no equipment," said Chergui.