She urged all parties to make "meaningful progress" by a November summit of East Asian leaders that President Barack Obama plans to attend in Cambodia.
In Indonesia's capital before heading to China, Clinton offered strong U.S. support for a regionally endorsed plan to ease rising tensions by implementing the code of conduct. Jakarta is the headquarters of ASEAN, and Clinton pressed the group to insist that China agree to deal with them as a bloc.
The stance puts the U.S. squarely at odds with China, which has become more aggressive in pressing its territorial claims with its smaller neighbors and wants the disputes to be resolved with each country, giving it greater leverage.
Clinton made her case in Jakarta on Tuesday in meetings with Indonesian President Susilo Bambang Yudhoyono and ASEAN secretary general Surin Pitsuwan, a day after she delivered the same message to Indonesian Foreign Minister Marty Natalegawa. Indonesia has played a leading role in putting the six-point plan together after ASEAN was unable to reach consensus on the matter in July.
Clinton said the U.S. is "encouraged" by the plan but wants it acted on particularly implementation and enforcement of the code of conduct, which has languished since a preliminary framework for it was first agreed upon in 2002. .
"The United States has a national interest, as every country does, in the maintenance of peace and stability, respect for international law, freedom of navigation, unimpeded lawful commerce in the South China Sea," Clinton told reporters at a news conference with Natalegawa.
"The United States does not take a position on competing territorial claims ... but we believe the nations of the region should work collaboratively to resolve disputes without coercion, without intimidation and certainly without the use of force," she said. "That is why we encourage ASEAN and China to make meaningful progress toward finalizing a comprehensive code of conduct in order to establish rules of the road and clear procedures for peacefully addressing disagreements."
Yet China on Tuesday expressed skepticism that the U.S. is neutral in the disputes.
"The U.S. has many times said it does not take a position," Chinese foreign ministry spokesman Hong Lei said on Tuesday. "I hope they will keep their promise and do more to help stability and not the opposite. The South China Sea dispute is a complicated thing. To China, the South China Sea dispute is about the sovereignty of some of the islands there. China, like other countries in the world, has the obligation to safeguard its territories."
China and a host of Southeast Asian countries, including the Philippines, Vietnam and Brunei, have overlapping claims to several small, but potentially energy-rich areas of the South China Sea.
In July, China angered the United States, as well as Vietnam and the Philippines, by creating a city and military garrison on a remote island 220 miles from its southernmost province intended to administer hundreds of thousands of square miles of water where China wants to strengthen its control over disputed islands. China, which also has disputes with Japan in the East China Sea, rejected the criticism.
In addition to the South China Sea, Clinton will be discussing the situation in Syria as well as the efforts to deal with Iran and North Korea's nuclear programs while she is in the Chinese capital.
Clinton is in China at the midpoint of an 11-day, six-nation tour of the Asia-Pacific region that started in the Cook Islands and Indonesia. After she leaves China, she will visit East Timor and Brunei before heading to Russia's Far East to represent the United States at the annual meeting of leaders from the Asia-Pacific Economic Cooperation forum in Vladivostock.