"The landmark arbitration ruling in July, which is binding, helped clarify maritime rights in the region," Obama told a summit of Asian leaders in Laos.
The comments are sure to draw ire from Beijing, which has taken an increasingly belligerent stance on claims in the strategically important waterway.
Obama has urged China to adhere to the rule of law and not take unilateral measures that could raise tensions.
"I recognise this raises tensions," Obama said referring to the ruling "but I also look forward to discussing how we can constructively move forward together to lower tensions and promote diplomacy and stability."
Even before Obama's comments, a dispute between the Philippines and China has overshadowed East and Southeast Asian summits in Laos.
Manila produced photos it said showed fresh construction activity at the flashpoint Scarborough Shoal, an accusation that was denied by Beijing and played down by Washington.
The area is just 230 kilometres from the main island of the Philippines, where US forces are stationed.
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