Kerry's two-day visit takes him to the capital, Manila, for talks with government officials and the business community.
As he did on his previous stop in Vietnam, Kerry will discuss maritime security with authorities in the Philippines, which also has territorial claims in the South China Sea.
"They will certainly discuss the specific issues pertaining to the South China Sea," a senior State Department official said.
These issues range from helping the Philippines strengthen its capacity for tasks such as maritime domain awareness, or finding out who is in its territorial waters and why, to legal issues over the country's challenge to China's claim on what is known as the nine-dash line, the official added.
"In the near term there's a need for practical measures to prevent incidents or manage them if they occur in a way that avoids escalation," he official said.
Regional tension with China has escalated over the territorial claims in the South China Sea. Separately, China and Japan are embroiled in a dispute over islands in the East China Sea.
The United States has said it is not taking sides in any of the disputes but in recent weeks has moved to defend its allies in the region against new moves by Beijing to control regional waters.
On Wednesday Kerry will travel to Tacloban in the central Philippines, the epicenter of super typhoon Haiyan, which decimated towns and villages on November 8. The storm has killed more than 6,000 people and displaced 4 million.
US marines and humanitarian groups have joined in a multi-million dollar relief effort to deliver aid to survivors.
While the United States has said it does not intend to open new military or naval bases in the region, Kerry will discuss ways that the U.S. can help respond quicker during disasters in the region such as typhoon Haiyan.
HEIGHTENED TENSION WITH CHINA
The heightened tension with China has raised concerns that a minor incident in the disputed sea could quickly escalate.
U.S. and Chinese warships narrowly avoided collision in the South China Sea last week, the U.S. Pacific Fleet said in a statement on Friday.
In Hanoi on Monday, Kerry pledged $32.5 million in new assistance to strengthen the capacity of Southeast Asian to patrol the seas.
Beijing's assertion of sovereignty over a vast stretch of the South China Sea has set it directly against Vietnam and the Philippines - the two countries Kerry is visiting - while Brunei, Taiwan and Malaysia also lay claim to other parts of the sea, making it one of Asia's biggest potential trouble spots.
On Monday, Kerry warned China to refrain from unilateral actions in the region, and particularly over the South China Sea, and urged countries to resolve their differences peacefully.
Kerry will also update government officials on talks between the United States and 11 other nations in the Pacific Rim on reaching a trade pact.
His visit to Southeast Asia comes as the United States strives for a trade deal with 11 countries in the Asia-Pacific. A Trans-Pacific Partnership (TPP) trade deal is the centerpiece of U.S. efforts to refocus attention on the fast-growing region.
(Editing by Clarence Fernandez)