The boy boarded an Istanbul-bound plane operated by Lebanon's national carrier, Middle East Airlines, on Wednesday.
He was discovered by the crew onboard after the plane had already taken off, when they realised there were more passengers on the aircraft than on the manifest they had been given, local media said.
"Widescale investigations are ongoing into the details of the incident and how the child passed through the security checkpoints and boarded the plane without being detected," airport authorities said in a statement published by the official National News Agency.
Local media said the boy was 13 years old, and had managed to sneak through the multiple security points in the airport and board the plane, taking a seat in business class.
His nationality and the purpose of his journey were unclear.
Passengers flying from Beirut's Rafik Hariri airport generally pass through at least five security points, including one before they enter the airport and a final examination of their documents by security at the departure lounge, before boarding flights.
In March, Transport and Public Works Minister Ghazi Zaiter told a press conference that there was a USD 1.4 million shortfall in funds needed to bolster security measures at the airport.
The boy's adventure prompted criticism from Walid Jumblatt, a leading political figure and head of the Druze minority, who linked it to the country's ongoing political stalemate.
Lebanon has been without a president for more than two years, with its parliament locked in a standoff between two rival political blocs.
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