A Japanese P-3C Orion and a Philippine navy islander flew on a search and rescue drill 50 nautical miles (92.6 kilometres) northwest of Palawan island, officials said.
While the flight was in the general direction of the resource-rich Reed Bank claimed by both the Philippines and China, officials refused to say if the planes flew directly over the area.
Following a similar flight on Tuesday, Chinese foreign ministry spokesman Lu Kang warned against hyping the navy drills, suggesting they could undermine stability in the region.
"I think it is important to continue HADR (humanitarian and disaster response), SAR (search and rescue) training with the Philippine Navy," he added.
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Philippine President Benigno Aquino's office also praised the drills.
"The Philippines has had these exercises before with our strategic partners," presidential spokeswoman Abigail valte said in a statement.
"It should not be taken as an affront to any other and is an expression of cooperation and learning from all those involved."
The surveillance plane crew did not observe anything unusual in the waters, Hamano told reporters.
Reed Bank lies about 85 nautical miles west of Palawan, within the Philippines' 200-mile exclusive economic zone.
An encounter between a Chinese vessel and a survey ship contracted by Filipino firm Philex Petroleum in 2012 has stalled exploration in the area.
The Philippines and Japan are in the middle of their second-ever naval joint manoeuvres this week, which followed historic exercises last month.
The two former World War II foes are strengthening their strategic partnership in the face of separate territorial rows with China.
China's claim over almost the entire South China Sea overlaps with those of the Philippines, Vietnam, Brunei, Malaysia and Taiwan.