"Absolutely no doubt in my mind that we're into the thousands" of dead, Toby Lanzer told reporters.
The official toll nationwide has stood at 500 dead for days, although numbers are feared to be far higher, aid workers say.
Witnesses whom AFP has spoken to recount a wave of atrocities, including an orchestrated campaign of ethnic mass killings and rape.
UN rights chief Navi Pillay said today that a mass grave had been found in the rebel-held town of Bentiu, while there were "reportedly at least two other mass graves" in the capital Juba.
Machar's forces were driven from the town of Bor today by the army, but still hold Bentiu, capital of the key oil-producing state of Unity.
Lanzer said the situation in Bentiu remained "tense."
"There are a lot of armed men, almost no civilians on the street," he said. "There are now well over 7,000 civilians within the UN base, where they've had to extend the perimeter."
