The report is the first detailed account of two incidents that have highlighted a pattern of gross abuses and atrocities committed during the year-old civil war in the world's youngest nation.
The UN also noted that nearly nine months after the events, "no perpetrator has been held accountable" for the killings.
In the April 15 attack on the northern oil-town of Bentiu, fighters backing South Sudan rebel leader Riek Machar murdered at least 287 civilians sheltering in a mosque, many of them traders and their families from neighbouring Sudan's Darfur region.
Fighters also took to the radio urging rival groups to be forced from the town and for men to rape women from the rival tribe.
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"Victims were deliberately targeted on the basis of their ethnicity, nationality or perceived support for one of the parties to the conflict," the UN said in a 33-page report.
Two days later on April 17, in the eastern town of Bor, a gang of heavily-armed men marched on the UN base, where hundreds of civilians had fled to for protection.
The "mob forcibly entered the protection site and went on a rampage of killing, looting and abductions", the report by the UN peacekeeping mission in South Sudan (UNMISS) said, adding the assault left at least 47 dead and was likely to have been "planned in advance".
At least 353 civilians were killed and another 250 were wounded in the two attacks, the UN said.
No overall death toll for the war has been kept, either by the government, rebels or the United Nations, although the International Crisis Group says it estimates that at least 50,000 people have been killed.
Some diplomats suggest it could be double that figure, while hunger and disease have killed thousands more.