Ban told South Sudanese President Salva Kiir he was pleased a recent government overhaul went by with few major national security issues.
Kiir brought back several ministers, including his petroleum minister. Former government spokesman Barnaba Marial Benjamin was promoted to foreign affairs minister in the overhaul following a Cabinet dismissal in late July. A government spokesman said the shake-up was long overdue.
Ban's office said in a statement Wednesday he told Kiir by phone he looked forward to working with the new administration but had lingering concerns about the state of affairs in Jonglei.
The secretary-general said Kiir's government was responsible for ensuring civilian lives are spared in ongoing fighting between government forces and rebel groups in the area.
John Prendergast, co-founder of the watchdog group Enough Project, said last month government forces were to blame for the violence.
"These terrible crimes occur because government forces believe they have the power to act with impunity," he said in a statement. "All senior army officials should be put on notice that attacks on civilians are completely unacceptable and will be severely punished."