African Union leaders face an unprecedented vote on deploying a 5,000-strong peacekeeping force despite Burundi's vehement opposition, but Ban was clear troops were needed to stem violence.
"Leaders who stand by while civilians are slaughtered in their name must be held responsible," Ban said, adding the crisis in Burundi required the "most serious and urgent commitment".
He said the UN backed the AU's proposal "to deploy human rights observers and to establish a prevention and protection mission" in Burundi.
AU commission chief Nkosazana Dlamini-Zuma opened the summit by commemorating AU peacekeepers killed in "efforts to silence the guns", amid fierce backroom debate on whether to send a new force to Burundi.
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Talks on the possible peacekeeping deployment are being held behind closed doors and it is unclear when a vote may be taken.
While the official theme of the African Union (AU) meeting is human rights, leaders are again dealing with a string of crises across the continent during two days of talks at the organisation's headquarters in the Ethiopian capital.
"Leaders in South Sudan have again failed to meet a deadline to form a transitional government," Ban said. "Instead of enjoying the fruits of independence, their people have endured more than two years of unimaginable suffering."
Neither Burundi's President Pierre Nkurunziza nor South Sudan President Salva Kiir are believed to be attending the summit.
"Leaders must protect their people, not themselves," Ban added.
AU Peace and Security Council chief Smail Chergui warned "the stakes are indeed high", but Burundi remained defiant in its opposition to a mission it calls an "invasion force".
Street protests, a failed coup and now a simmering rebellion began when Nkurunziza announced his intention to run for a controversial third term, which he went on to win in July elections.
Hundreds have died and at least 230,000 have fled the country in the months since.