In the main mosque alone, "more than 200 civilians were reportedly killed and over 400 wounded," the UN mission in the country said, adding there were also massacres at a church, hospital and an abandoned UN World Food Programme (WFP) compound.
Fighters took to the radio urging rival groups to be forced from the town and for men to rape women from the opposition ethnic group.
The conflict has also taken on an ethnic dimension, pitting President Salva Kiir's Dinka tribe against militia forces from Machar's Nuer people.
UN human rights investigators said that after rebels wrested Bentiu from government forces in heavy battles last Tuesday, the gunmen spent two days hunting down those they believed opposed them.
Both South Sudanese and Sudanese -- some from the war-torn Darfur region -- were killed, the UN peacekeeping mission in South Sudan (UNMISS) said in a statement.