"I am deeply concerned about the recent rise in violence by armed groups in the eastern Democratic Republic of the Congo and the rise of terrorist groups in the Sahel and elsewhere," Guterres said at the start of the annual African Union (AU) summit in Addis Ababa.
African leaders are meeting to push for ceasefires in the Sahel hit by putschists and the eastern DRC where the M23 militia has seized swathes of territory and sparked a diplomatic row between Kinshasa and Rwanda, which is accused of backing the rebels.
There has been a wave of coups since 2020 in the Sahel countries of Mali, Guinea and Burkina Faso.
"The mechanisms for peace are faltering," Guterres warned.
Nevertheless, he urged the bloc to "continue to battle for peace."
The U.N. chief said Africa faced "enormous tests... on virtually every front," adding that the continent was bearing the brunt of multiple crises it had no hand in generating, including the Russian invasion of Ukraine and climate change.
"The brutal injustice of climate change is on full display with every flood, drought, famine and heatwave endured on this continent," he said.
At a mini-summit on Friday, leaders of the seven-nation East African Community called for all armed groups to withdraw from occupied areas in the eastern DRC by the end of next month.
Guterres met with several African leaders on Friday, including Rwandan President Paul Kagame, to discuss in particular the crisis in the Congo.
Junta-ruled Mali, Burkina Faso and Guinea, which have been suspended from the AU, cannot participate in this weekend's summit.
But diplomats of the three nations are in Addis Ababa to push for readmission.
"I endorse your call for the restoration of civilian and democratically elected governments in Burkina Faso, Guinea, Mali and Sudan," Guterres said.
The two-day summit, bringing together the 55 countries on the continent, also aims to jumpstart a faltering free trade deal.
Azali Assoumani, the 64-year-old leader of the small Indian Ocean archipelago of the Comoros, succeeded Senegal's Macky Sall for the 12-month rotating leadership of the continental body.