Police isolated and surrounded the Saudi flight after it landed on Tuesday afternoon just after one of its pilots released a distress signal indicating a hijack incident was underway, the Philippine aviation authority said in a statement.
Hundreds of passengers aboard the Boeing 777 flight from the Red Sea city of Jeddah were forced to remain on the plane for more than two hours, but were let off about 5:00pm (0900 GMT) after it was confirmed there was no threat.
In Saudi Arabia, an airline spokesman also told AFP there was no security threat.
There were 410 passengers on board, plus four pilots and 17 crew members, airport general manager Ed Monreal told reporters.
Many of them were returning from the annual Islamic pilgrimage (Hajj) in Saudi Arabia.
One of the passengers, Aida Majud, said they were not told why they were being kept on the plane.
The carrier is known as Saudia.
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