In a joint statement Obama, Tony Abbott and Shinzo Abe urged "freedom of navigation and over-flight, and the peaceful resolution of maritime disputes in accordance with international law".
The trio said they were committed to deepening their already strong security cooperation in the Asia-Pacific, which comes amid China's increasingly assertive expansion in the region.
Beijing is locked in dispute with four Southeast Asian countries over lonely outcrops in the South China Sea, and with Japan over another set of islets.
"They noted that this partnership rests on the unshakable foundation of shared interests and values, including a commitment to democracy and open economies, the rule of law, and the peaceful resolution of disputes," they said in the statement.
US President Obama, in a speech in Brisbane yesterday, warned of the dangers of outright conflict in Asia but vowed that Washington would remain anchored in the region.
He said while there had been stunning economic progress in Asia since World War II, there were also genuine dangers, saying there were "disputes over territory -- remote islands and rocky shoals -- that threaten to spiral into confrontation".
On Friday, Japanese Prime Minister Abe said he wanted deeper defence ties with the United States and Australia to ensure peace and throughout the Asia-Pacific region.
