The Philippines infuriated China in March by asking a United Nations tribunal to declare Beijing's territorial claims in the South China Sea a violation of international law.
China claims almost all of the sea, a vital avenue for world trade that is also believed to harbour vast oil and gas reserves.
But its claims overlap in parts with those of the Philippines, as well as Brunei, Malaysia, Vietnam and Taiwan.
"We wanted to maintain the moral high ground in light of the case we filed at the (UN) arbitration tribunal regarding the West Philippine Sea," Valte said, using the Filipino name for the area.
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"We chose... To ease tensions and avoid any incident that may be construed as ramping up tensions or trying to provoke any of the claimant countries," Valte said over government radio today.
The runway is used mainly by military aircraft to resupply the Filipino troops guarding the island and nearby rocks, as well as a small community of Filipino civilians living on Thitu.
The upgrade plans were suspended by Aquino "sometime in the middle of 2014", Valte said.
The airstrip project, as well as acquisitions of navy vessels, were part of Aquino's efforts to upgrade the capability of the Philippine military, one of the most poorly equipped in the region.
The two countries have been involved in several tense confrontations in the South China Sea in recent months.
Valte dismissed suggestions that suspending the airstrip project would allow China to ramp up its increasingly assertive efforts to stake its claims in the South China Sea.
"In our view, it will not weaken our position," she added.