"Japan remains committed to dealing with any outstanding issues in a calm and peaceful manner," Noda said at a meeting of political leaders in the Cambodian capital Phnom Penh.
Noda said Japan is promoting a "mutually beneficial relationship based on common strategic Interest," a report by the Japanese news agency Kyodo said.
International law in resolving territorial rows in the South China Sea should be paramount, he told delegates to the Association of Southeast Asian Nations meeting.
The Kyodo report said Noda's remarks reflect Japan's vigilance of China's rapid naval expansion in resource-rich Asian waters, an issue which should be a "common concern for the international community."
He also stressed that the Japan-China relationship is "one of the most important bilateral relationships for Japan."
But that relationship has come under increasing political tension in the past year as Beijing and Tokyo sustain a war of words over Japan's control the Senkaku Islands, called the Diaoyu Islands by the Chinese.
Ownership of the Senkakus, as with other disputed islands in the South China Sea, brings with it rights over the increasingly important oil and natural gas fields on the seabed, as well as fishing rights.
Japan and China have had high-level talks over the islands amid wary Japanese naval patrols around the rocky outcrops 100 miles north of Japan's Ishigaki Island.
Japan has complained of increasing incursions by Chinese patrol vessels and fishing boats into territorial waters around the islands.
Relations between Tokyo and Beijing have been strained particularly since Noda's government purchased some of the uninhabited islets from their Japanese owner in September.
Beijing complained about the purchase immediately before and after the deal had been signed.
"The Japanese government single-mindedly took the action of illegally purchasing the Diaoyu Islands, which is a gross violation of China's territorial sovereignty and hurt the Chinese people's feelings," a Chinese foreign ministry spokesman said at the time.
The Senkaku Islands are claimed also by Taiwan, which, like Japan and China, isn't a direct member of ASEAN.
ASEAN members are Brunei, Cambodia, Indonesia, Laos, Malaysia, Myanmar, the Philippines, Singapore, Thailand and Vietnam. China and Japan as well as South Korea, India, Australia and New Zealand are regional partners of ASEAN.
Japan aims to host a special summit with ASEAN leaders next year to coincide with the 40th anniversary of the Japan-ASEAN relationship, the Japanese Foreign Ministry said.
The two leaders spent most of their meeting at the Peace Palace discussing human rights, said Ben Rhodes, U.S. deputy national security adviser.
Cambodia is the last leg of Obama's three-country tour that started in Thailand then progressed to Myanmar.
In Yangon, Myanmar, Obama said the road to democracy is a challenge but Myanmar is an example for the world.
"I stand here with confidence that something is happening in this country that cannot be reversed and the will of the people can lift up this nation and set a great example for the world," Obama, the first U.S. president to visit Myanmar, told about 1,500 people at the University of Yangon.
"And you will have in the United States of America a partner on that long journey."