In a meeting with two top Chinese officials, who are visiting Washington to attend the US-China Strategic and Economic Dialogue, Obama also expressed his disappointment over handling of the case of Edward Snowden, a former CIA contractor who unveiled details of US online snooping.
Obama met with China's Special Representatives to the US-China Strategic and Economic Dialogue, Vice Premier, Wang Yang and State Councilor Yang Jiechi at the White House after the conclusion of the dialogue.
Tensions have steadily risen between China and Japan, recently in the East China Sea.
The Philippines and Vietnam have also charged that China has used assertive means to exert claims in the South China Sea.
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China claims nearly all of the sea, even waters approaching the coasts of neighbouring countries. ASEAN members Brunei and Malaysia, as well as Taiwan, also have competing claims to parts of the sea.
"He added that the United States would continue to speak out in support of international norms such as the protection of universal human rights. The President expressed his disappointment and concern with China's handling of the Snowden case," the White House said.
"The President reiterated concerns about cyber-enabled theft of trade secrets, and welcomed joint efforts to develop rules and norms of behaviour in cyberspace," it said.
During the meeting Obama underscored the importance of increasing practical cooperation on regional and global challenges while constructively managing our differences and areas of competition.
Obama discussed the economic reforms underway in China and their compatibility with policies the administration is pursuing at home.
"He (Obama) also welcomed China's important new commitment to open its economy to US investment in a bilateral investment treaty that it is negotiating with the US," the White House said.