Vladimir Voronkov, the under-secretary general for counter-terrorism, is the highest level UN official to visit Xinjiang, which activists have described as an open air prison, deprived of religious freedom.
UN spokesperson Farhan Haq confirmed that Voronkov, a Russian diplomat, was on an official visit to China, but did not provide details of his itinerary.
Haq stressed that the UN counter-terrorism office works to ensure that measures used to fight terror respect human rights.
Beijing argues that internment camps in Xinjiang are "vocational training centers" to steer people away from extremism and reintegrate them, in a region plagued by violence blamed on Uighur separatists or militants.
Voronkov's visit to Xinjiang, first reported by Foreign Policy magazine, drew sharp criticism from rights activists.
"The UN allowing its counterterrorism chief to go to Xinjiang risks confirming China's false narrative that this is a counterterrorism issue, not a question of massive human rights abuses," Louis Charbonneau, the UN director for Human Rights Watch, told AFP.
UN rights chief Michelle Bachelet asked Beijing in December for permission to carry out a fact-finding mission in Xinjiang, but has been left waiting.
Earlier on Thursday, China's new ambassador to the United Nations in Geneva, Chen Xu, said the UN high commissioner for human rights would pay a visit when "we can find a time which is convenient to both sides."
China has insisted that the fate of the estimated one million Uighurs, ethnic Kazakhs, Kyrgyz, and other Muslims is an internal matter.
At the request of the United States and other Western countries, UN Secretary-General Antonio Guterres in May raised the plight of the Uighurs during his visit to China.
Guterres told Chinese Foreign Minister Wang Yi that "human rights must be fully respected in the fight against terrorism," according to the UN.
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