Obama flew into Manila from Malaysia, hours after the allies signed a new defence agreement allowing more US troops and defence hardware to rotate through the Philippines, part of a US rebalancing of military power towards rising Asia.
Obama was also preoccupied with the crisis in Ukraine, which has shadowed him around Asia for the last six days, as the United States and Europe gear up to slap new sanctions on Russia, likely within hours.
Obama was due to meet Philippine President Benigno Aquino, participate in a joint press conference and be honoured at a state dinner.
Anti-China sentiments run high in the Philippines, which is locked in a showdown with the Asian giant over disputed atolls in the South China Sea, part of a proliferation of maritime hotspots that has stoked Asian tensions.
During a tour that has taken him to Japan, South Korea and Malaysia, Obama has repeatedly warned that small nations should not be bullied by larger ones, a clear reference to China's increasingly sharp geopolitical elbows.
"Disputes need to be resolved peacefully, without intimidation or coercion, and... all nations must abide by international rules and international norms," Obama said in Malaysia Sunday.
- Simmering disputes -
Opening his trip, Obama made clear that US defence treaties with Japan did cover disputed islands long administered by Tokyo in the East China Sea, which are known as the Senkakus in Japan and Diaoyus in China.
The Philippines has its own territorial disputes with China in the South China Sea -- notably over the Second Thomas Shoal, an outpost in the remote Spratly Islands.
US officials have not been so specific over their obligations towards Manila on territorial disputes -- but it is clear they do not believe they are covered by the American Mutual Defense Treaty with the Philippines.
"With respect to some of the difficult territorial issues that are being worked through, it is hard to speculate on those because they involve hypothetical situations in the South China Sea," said deputy national security advisor Ben Rhodes.
"The US-Japan agreement has very specific coverage of territory under Japanese administration.
"Some of the disputes in the South China Sea raise more hypothetical circumstances."
In essence, the difference lies in the fact that Japan already administers the Senkakus/Diaoyus while the status of other islands and reefs is disputed -- even though they lie within the Philippines' internationally mandated exclusive economic zone and far closer to Filipino landmass than Chinese.
Brunei, Malaysia, and Vietnam, as well as Taiwan, also have overlapping claims to the sea, believed to contain vast deposits of natural gas and oil.
Obama has repeatedly stressed that despite Beijing's territorial disputes with its allies, his Asia rebalancing strategy is not aimed at containing China's rise to regional, and perhaps global superpower status.
But US officials also make clear that they blame China for hiking tensions in the region over claims often well outside its territorial waters.
"We oppose the use of intimidation, coercion or aggression by any state to advance their maritime territorial claims," said Evan Medeiros, senior director for Asia at the National Security Council.
- US 'rebalance' to Asia -
The Philippines has accused China of becoming increasingly aggressive in staking its claims to the sea, and has called on the United States for greater military as well as diplomatic support.
The new agreement, signed in Manila on Monday by Philippine defence minister Voltaire Gazmin and US ambassador Philip Goldberg, will not allow Washington to establish a permanent base in the Philippines or bring in nuclear weapons to the country.
But it represents a new era in defence ties, allowing more of the high-profile war games that are regularly conducted by the long-time allies and for some US military hardware to be stationed on Filipino soil.
The Philippines hosted two of the largest overseas US military bases until 1992, when Manila voted to end their lease at a time of growing anti-US sentiment.
With rising regional disquiet over the implications of China's rise, the Philippines has sought greater military ties with Washington in recent years.
In comments to local television network ABS-CBN ahead of his arrival in Manila, Obama sought to reassure the Philippines about US support, referring to a 1951 mutual defence treaty between the two nations.
"The United States stands by its allies, in good times and in bad," Obama said.
"In fact, one of the main purposes of my visit will be to reaffirm our treaty commitments to the Philippines and to make it clear that just as we've relied on each other in the past, we can count on each other today."