The United Nations High Commissioner for Human Rights, Mary Robinson, has warned China not to use the American-led campaign against terrorism as a pretext to suppress ethnic minority groups.
Speaking on the first day of a trip to China, she said she was worried about the Uighur population in the Western province of Xinjiang.
She also expressed concern about the situation in Tibet.
Mary Robinson torture was "widespread" in China
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China later denied there were abuses in the two regions. A foreign ministry spokesman said the real problem was sabotage carried out by separatist groups.
Beijing has called for international support for its campaign against ethnic Uighur Muslim separatists in Xinjiang.
It has also accused supporters of Tibet's exiled spiritual leader, the Dalai Lama, of terrorist activities.
Coinciding with her visit, the Chinese State Council has released a white paper on Tibet, which argues that Tibetans have seen improvements in wealth and freedom under Chinese rule.
Balance
Mrs Robinson's comments came after she signed an agreement with China on improving human rights education among police, judges and lawyers.
She said: "It is necessary to take measures, but there must be also a very clear balance."
"I am worried specifically about the Uighur population in the province of Xinjiang [and] I am worried about the situation in areas such as Tibet."
Mrs Robinson said it was difficult to see how a balance between anti-terrorism and anti-discrimination action could be struck because terrorism itself is not defined.
She also said she would press Beijing to set a date for a visit by the UN rapporteur on torture.
Chinese Vice Foreign Minister Wang Guangya said the agreement showed the Chinese government was serious about co-operating with other countries and with UN agencies.
Mrs Robinson is also due to meet President Jiang Zemin during her two-day visit.