The rebels have taken another town from government troops after seizing Bentiu last week.
"We are horrified by reports out of South Sudan that fighters aligned with rebel leader Riek Machar massacred hundreds of innocent civilians last week in Bentiu," said spokesman Jay Carney in a statement.
The rebels unleashed two days of ethnic slaughter last week as they hunted down civilians sheltering in mosques, churches and a hospital, killing dozens on the roadside, according to the United Nations.
The deceased have been buried in mass graves and refugee camp populations have surged, it added.
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"We are equally appalled by the armed attack last week at the UN Mission in South Sudan site in Bor that killed at least 48 civilians and injured dozens more," Carney said.
The White House called on President Salva Kiir and Riek Machar to "make clear that attacks on civilians are unacceptable, perpetrators of violence on both sides must be brought to justice, and the cycle of violence that has plagued South Sudan for too long must come to an end."
South Sudan's army has been fighting rebels loyal to sacked vice president Riek Machar since the unrest broke out more than four months ago.
The conflict has taken on an ethnic dimension, pitting President Salva Kiir's Dinka tribe against militia forces from Machar's Nuer people.