"The secretary-general finds it unacceptable that the Sri Lankan authorities have failed to prevent the disruption of the normal functioning of the United Nations offices in Colombo as a result of unruly protests," Ban Ki-moon, the UN secretary-general, said in a statement.
Farhan Haq, a spokesman for Ban, said the secretary-general hopes to reopen the office soon.
"What he wants is for our vital work to continue," Haq told Al Jazeera. "Sri Lanka needs to allow our work to proceed without hindrance, the way they have done in the past."
The protests are believed to have the tacit approval of the Sri Lankan government. Wimal Weerawansa, the housing minister, has led many of the demonstrations.
Earlier this week, Weerawansa accused the UN of conspiring to "hunt down our soldiers".
Rajiva Wijesinha, a Sri Lankan member of parliament, insisted that Colombo was capable of carrying out its own investigation.
"There might be some people who say this is slow, but it's a damn sight quicker than that of many countries," he told Al Jazeera.
"One doesn't want to point fingers, but the British finally looked into Bloody Sunday 28 years afterwards. The problem here is that people around the world want to try and accuse us of war crimes."
The UN has said that at least 7,000 Tamil civilians were killed in the final stages of the decades-long war last year. Human-rights groups have accused the Sri Lankan government of committing regular human rights abuses throughout the conflict.
Amnesty International and other human rights groups accused the government of intentionally shelling civilians, bombing hospitals and food distribution points, and opening fire in declared no-fire zones.
The groups also accused the government of shelling hospitals filled with wounded civilians.
The Sri Lankan government routinely denies those allegations, and it has ignored calls for an investigation.