In a Christmas Day radio and video message to the people of South Sudan, Ban called ethnic attacks a "grave violation of human rights" and reiterated that those responsible would be "held accountable."
"South Sudan is under threat - but South Sudan is not alone," Ban said, a day after the UN Security Council voted to send an additional 6,000 peacekeepers to the nation in a bid to stave off civil war.
Thousands have flooded UN bases in recent days, seeking shelter from the outburst of violence between government troops and forces loyal to Machar, a former vice president who was sacked in July.
Kiir has accused Machar of attempting a coup, a charge his former deputy denies. The ensuing unrest has taken on an ethnic dimension, pitting members of Kiir's Dinka tribe against Machar's Nuer.
"I once again call on the country's leaders to settle their differences peacefully - and I underscore their responsibility to protect civilians," Ban said.
"We are strengthening the United Nations presence and will do our best to stop the violence and help you build a better future for all," Ban said at the end of his message.
The UN reinforcements will nearly double the size of the UN mission in South Sudan (UNMISS), allowing for up to 12,500 soldiers and 1,300 police.
Both Kiir and Machar have indicated a willingness to come to the negotiating table, after days of international efforts to put a halt to the violence in the country, which won independence from Sudan to much fanfare just two years ago.
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