Beijing voted against a resolution at the UN Human Rights Council that said abuses in Myanmar indicated "the very likely commission of crimes against humanity".
"It will probably complicate the issue and have some negative influence on implementing the repatriation agreement between Myanmar and Bangladesh," Chinese foreign ministry spokesman Geng Shuang said during a regular press briefing, referring to a deal signed in November to start returning Rohingya refugees within two months.
China was one of only three countries that opposed the text, which passed Tuesday with 33 of the council's 47 member states voting in its favour.
A army-led crackdown has forced some 626,000 people to flee the northern Rakhine state and cross the border into squalid camps in Bangladesh in recent months, and left hundreds of villages burned to the ground.
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Myanmar's military vehemently denies accusations by the UN and the US that it has committed ethnic cleansing against the Rohingya.
But in his address to Tuesday's special council session, UN High Commissioner for Human Rights Zeid Ra'ad Al Hussein went even further by suggesting that "elements of genocide may be present".
The proposal was "warmly received by relevant parties," Geng said Wednesday.
Myanmar leader Aung San Suu Kyi visited Beijing last week, meeting with President Xi Jinping and attending a global meeting of political organisations hosted by the Chinese Communist Party.
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