The displaced have given accounts of the killing of civilians, homes destroyed and sexual violence.
The displaced, primarily from towns south of the capital Juba in Central Equatoria state, have given accounts of the killing of civilians, homes destroyed and sexual violence, said Adama Dieng.
"President Salva Kiir has made a commitment to end the violence and bring about peace, yet we still see ongoing clashes, and the risk that mass atrocities will be committed remains ever-present," said the special adviser in a statement.
Dieng said he was particularly alarmed at the situation in Kajo-Keji where fleeing civilians have said they fear mass violence.
After several delays, a team from the UN peacekeeping mission arrived in Kajo-Keji on Sunday to report on the situation.
After gaining independence from Sudan in 2011, South Sudan descended into war in December 2013, leaving tens of thousands dead and more than three million people displaced.
There is growing alarm over the humanitarian crisis in the country where more than six million people -- half of South Sudan's population -- are in need of urgent aid. Humanitarian organizations expect this number to rise by 20 to 30 percent in 2017.