The passengers of Saudi Arabian Airlines flight SV 872, which took off from Jeddah shortly before midnight (local time), were being checked one-by-one to confirm whether or not it had been hijacked, mirror.uk reported.
The alarm followed the pilot having reportedly pressed a hijack 'panic button'.
Before landing, the plane's pilots reportedly told the Manila airport control tower that the plane was "under threat" and asked for emergency assistance, saying emergency 4 — a code that could mean possible hijacking in airline jargon, Xinhua news agency reported.
TV footage showed emergency service vehicles scrambled as the plane touched down around 3 pm on Tuesday, escorting the jet to a secure area.
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The aircraft was being held "in total isolation", according to media reports.
Airport authorities were trying to establish communication with the pilots and were yet to issue an official statement on the incident.