The flight, operated by Indonesian flag carrier Garuda, was scheduled to take off Tuesday morning from the western island of Sumatra and head for Jakarta.
But the pilot of the Boeing 737, which was carrying 156 passengers, decided not to take off after noticing a problem with the controls, according to Garuda.
"An investigation found that the incident occurred because the plane's electronic engine control suffered a technical problem after an insect got into a pitot tube," airline spokesman Benny Butarbutar said in a statement.
Another Garuda official confirmed it was a bee that became trapped in the pitot tube, a vital piece of equipment which measures airspeed.
The airline did not say whether the bee survived the ordeal.
After being repaired, the plane took off and landed safely in Jakarta on Tuesday afternoon.
Butarbutar insisted the incident was beyond the airline's control, but said that passengers had nevertheless been given money as compensation.
It is not the first time an errant bee has caused an aviation incident.
Last June, British budget airline Flybe was forced to abandon a flight shortly after take-off when a bee became lodged in an instrument.
The U-turn came after the move, announced Tuesday, baffled aviation analysts, with one describing it as "ludicrous".
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