The missing jet was one of two S211 aircraft sent to the Philippine-held Kalayaan islands group in the Spratlys to search for 26 Filipino crewmen whose fishing vessel capsized Thursday in stormy weather.
One jet returned to western Palawan province, but the other did not, said air force spokesman Lt. Col. Epifanio Panzo.
"We don't know what happened. We don't know if it crashed. We lost contact ... it's missing," he said.
Panzo said the two jets took off at 8:45 a.m. with enough fuel for four hours of flight. He said contact with the missing jet was lost less than two hours after takeoff.
At least 10 people have been killed since Typhoon Mitag began battering the central region over the weekend, before slamming ashore in the northeastern corner late Sunday. A lingering tropical storm, Hagibis, re-entered the country's waters Monday and was expected to lash Palawan, near the Spratlys, on Tuesday, forecasters said.
Government forecasters also were monitoring a new low pressure area that could develop into a storm over the Pacific Ocean and affect the Philippines in a few days.
The Philippines, Vietnam, China, Taiwan, Malaysia and Brunei have overlapping claims in the largely uninhabited Spratly islands, which are believed to be rich in oil and natural gas. The islands and atolls also straddle busy sea lanes and are rich fishing grounds.
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