Speaking on board the visiting USS Fitzgerald, Clinton signed a declaration marking the 60th anniversary of a US Security Treaty with the Philippines.
"The United States is working with our Filipino allies to ensure that we can meet threats like proliferation and terrorism, and to support the Philippines particularly in the maritime domain as you move to improve your territorial defence and interdiction capability," she said in a report by AFP.
The joint declaration called for "freedom of navigation, unimpeded lawful commerce and transit of people across the seas".
In his response, Philippine Foreign Affairs Albert del Rosario said the statement "attests to the vitality of our alliance, especially at a time when the Philippines is facing challenges on its territorial integrity in the West Philippine Sea", the report added.
The Philippines is seeking the support of members of the Association of Southeast Asian Nations (ASEAN) for its proposal on a China-ASEAN dialogue instead of China dealing with individual countries involved in the territorial claims.
The Philippines has proposed a "Zone of Peace, Freedom, Friendship and Cooperation( ZoPFFC)," and called on other other ASEAN member-nations to support the proposal which intends to define which areas are disputed territories and which ones are the sovereignty of the country.
ASEAN has not responded positively to the Philippine proposal which was seen by observers as a first sign of discord in the 10-member Asian block.
"We have been given the impression that political and economic considerations have hindered a fruitful and mutually acceptable outcome on the discussions of the ZoPFFC," Rosario said in a statement in Manila
Tuesday that was read by his deputy at an ASEAN foreign ministers meeting in Bali.
"ASEAN must play a decisive role at this time if it desires to realize its aspirations for global leadership." del Rosario added.