"Absolutely no doubt in my mind that we're into the thousands," Toby Lanzer said. (Agencies)
The official toll nationwide has stood at 500 for days, although numbers are feared to be far higher, aid workers say.
UN rights chief Navi Pillay said 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.
The grim discoveries follow more than a week of escalating battles between troops loyal to President Salva Kiir and those backing his rival Riek Machar, a former vice-president who was sacked in July.
Machar's forces were driven from the town of Bor on Tuesday 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."
Fighting has spread to half of the young nation's 10 states, with hundreds of thousands fleeing to the countryside, prompting warnings of an imminent humanitarian disaster.
"Absolutely no doubt in my mind that we're into the thousands," Toby Lanzer said.