Detectives from Victoria Police Crime Command are investigating an incident in Avalon on Thursday afternoon.
Officers were called to the airport about 2.20pm after a male had entered a commercial flight armed with a firearm.
A 17-year-old boy was detained by crew and passengers on the flight.
At this stage officers believe the teen managed to get onto the tarmac after breaching a security fence.
Police located two bags and a vehicle belonging to the boy.
The Bomb Response Unit were called to assist with the bags as a safety precaution.
Fortunately no one was physically injured during the incident.
The 17-year-old from the Ballarat region remains in custody and will be interviewed by police.
The investigation into the incident is ongoing but there is no ongoing threat to the community.
Anyone with information about the incident is urged to call Crime Stoppers on 1800 333 000 or visit www.crimestopersvic.com.au