The rebel Seleka coalition seized control of the government in the Central African Republic. Ousted President Francois Bozize fled to Cameroon and rebels suspended the constitution.
Ban told the Economic Community of Central African States that security has deteriorated in CAR despite efforts by African leaders.
"I note, with concern, the consequences of insecurity and the aggravation of a humanitarian situation that is already precarious across the country, particularly in Bangui," he said in a statement to leaders gathered in neighboring Chad.
Ban said there were emerging reports of rape, the use of child soldiers and other grave violations of international laws.
Aid groups say there's little electricity or running water in Bangui.
Georgios Georgantas, head of the Red Cross delegation in CAR, said the capital was relatively calm. Volunteers were back at work "but the need for security for our personnel and our facilities is as urgent as ever," he said.
The Red Cross said it helped bury around 30 unidentified bodies in the capital since March 23.