Rice is the highest-level US official to visit the capital since an international tribunal this month rejected China's vast territorial claims in the South China Sea -- infuriating Beijing and fuelling tensions with Washington.
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Her trip is intended to prepare for a visit by President Barack Obama to a G20 summit in the city of Hangzhou in September.
The Permanent Court of Arbitration in The Hague on July 12 denied the legal basis for Beijing's claim to nearly all of the sea, parts of which are also claimed by neighbouring nations.
In recent months Washington has sent naval vessels close to reefs and outcrops claimed by Beijing to assert the principle of freedom of navigation, sparking anger in China which has built a series of artificial islands capable of supporting military operations.
Despite tensions, the two countries have tried to improve communication between their militaries in hopes of minimising misunderstandings that could lead to conflict.
"We should be honest with ourselves that deep down in this relationship we're still faced with obstacles and challenges," Fan Changlong, vice chairman of China's Central Military Commission, told Rice, adding that military ties had been "impacted by some complicated and some sensitive factors".
China to hold drills in South China Sea ahead of court ruling
"If we do not properly handle these factors it will very likely disturb and undermine this steady momentum of our military-to-military relationship," he warned.
Rice noted that "risks of unintended consequences" of the two countries' forces operating in ever-closer proximity had been reduced thanks to better communication and other confidence-building measures.
But despite progress, "we have challenges and differences to discuss and to manage", she said.
At a meeting with State Councillor Yang Jiechi -- China's top foreign policy official -- earlier in the day, Rice had called for "candour and openness" in facing such challenges and made positive remarks about US-China cooperation on climate change, global health issues and nonproliferation.
She is also scheduled to meet President Xi Jinping.
China rejected the tribunal ruling on the South China Sea as "waste paper" and asserted its right, if it chooses, to establish an Air Defence Identification Zone controlling flights over the area.
Tribunal rules against Beijing in South China Sea dispute
At a regional summit in Vientiane Monday Southeast Asian nations avoided rebuking Beijing or mentioning the ruling, in a joint statement seen as a victory for China.
Rice made no direct mention of the tribunal verdict. But the topic nonetheless looms large over her four-day trip, which also includes a stop in Shanghai to meet business leaders.
In opening remarks of his own, Yang said US-China relations this year had been "generally stable" and urged increased cooperation even in the face of disagreements.
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