The seven displaced persons were living in the base in the northeast town of Malakal where violence between the ethnic Dinka and Shilluk communities broke out overnight and continued into the day, he said.
Ban condemned the fighting and expressed concerns about the rise of ethnic violence in the more than two-year conflict.
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The UN chief reminded all sides that attacks on UN peacekeeping bases can constitute a war crime and urged them to implement a peace deal signed in August.
Fighting has continued in South Sudan despite the peace accord. Thousands have died and more than 2.3 million have been driven from their homes.
Nearly 200,000 civilians have sought shelter in the UN mission's eight compounds in South Sudan since the conflict began.
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