Ban called on President Salva Kiir to make "an offer of dialogue" to his opponents to end deadly fighting that erupted Sunday, said UN spokesman Martin Nesirky.
Salva Kiir has accused Sudan People's Liberation Army troops loyal to his former vice president Riek Machar of staging a coup attempt in the world's youngest nation.
Ban held telephone talks with Salva Kiir on the unrest in which dozens of soldiers are said to have died in Juba. The UN Security Council was to hold emergency talks on South Sudan later today.
Ban said "that up to 13,000 civilians have sought refuge at the UN compounds in Juba; a large number of them are women and children," the spokesman added.
Ban called for an immediate halt to hostilities and for Salva Kiir's government "to extend an offer of dialogue to its opponents and to resolve their respective differences peacefully."
"He said he was counting on the president to exercise real leadership at this critical moment, and to instill discipline in the ranks of the SPLA to stop this fighting among them," the spokesman said.