"Our primary message has been to make sure violence is avoided," Obama told reporters in Beijing on the sidelines of an Asia-Pacific leaders' meeting.
Protesters have held continuous street rallies in the semi-autonomous city for more than a month, demanding free leadership elections in 2017.
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Obama avoided voicing explicit support for the protest goals, saying that relations between China and Hong Kong were "in the process of transition" but adding: "We don't expect China to follow an American model."
"We're going to continue to have concerns about human rights," he continued.
"We believe in freedom of speech, we believe in freedom of association, we believe in openness in government."
Obama is making his first trip to China in five years to take part in a summit of Asia Pacific Economic Cooperation (APEC) leaders in Beijing.
China and the United States have already jousted in Beijing over differing visions of Asia-Pacific trade integration, adding to ongoing discord over commerce, human rights, cyber-espionage, and territorial disputes.
The White House has said it expects "candid and in-depth conversations" between Obama and China's President Xi Jinping, though few expect any major breakthroughs.
The US last month called for a "swift, transparent and complete" investigation into the beating of a handcuffed Hong Kong democracy protester by plainclothes police, one of several clashes during the mostly-peaceful protests.
Demonstrators have been camped out at three major road junctions since September 28 in the former British colony, which enjoys civil liberties not seen on the Communist-ruled mainland.
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