Police were called to Avalon Airport near Geelong, in Victoria, on Thursday afternoon following reports a male wielding a firearm attempted to board the Jetstar flight.
Victoria Police Superintendent Michael Reid told reporters the 17-year-old from Ballarat allegedly climbed through a hole in the airport's security fence before making his way on foot to the plane.
The teenager was charged with multiple offences including unlawfully taking control of an aircraft, orchestrating a bomb hoax and possessing a firearm.
He was remanded in custody to face Victoria's Children's Court on Friday.
Avalon Airport has fully reopened with all flights operating as normal on Friday morning.
The Sydney-bound flight was carrying about 150 people. No one was hurt during the incident.
Avlaw Aviation Consulting chair Ron Bartsch described the incident as "simply not acceptable" and said all airports should have the same level of security.
"It's not inconceivable that someone with some wire cutters or whatever can cut through a fence, so it makes a mockery of having sophisticated scanning and security systems if people can simply bypass it," he told ABC Radio Melbourne.
"The airline has their own security training and their own security experts, but that's got to marry up and integrate with the security on the tarmac, ramp operations and throughout the airport.
"Any breakdown in the system can cause something like this, irrespective where it happens - at the airline level or at the airport level."
The airport's chief executive Ari Suss said the organisation was working with Victoria Police.
"As part of our ongoing commitment to security, we have implemented further measures across the airport, including within the terminal and surrounding areas," he said in a statement.
"We continue to work closely with authorities to maintain a safe and secure environment for all travellers."
The probe is being carried out by crime squad investigators with no involvement from the force's counter terrorism unit.
The teen allegedly tried to climb the front stairs into the plane cabin but was noticed by passengers and subsequently overpowered by three civilians, Supt Reid said.
"This would have been a very terrifying incident for the passengers of that plane and Victoria Police really commend the bravery of those passengers who were able to overpower that male," he said.
Passenger Barry Clark tackled the teen as he spoke to a flight attendant.
"Before we knew it, a shotgun appeared and I was worried about it being shot," Mr Clark told the public broadcaster.
"All I could do was push her out of the way, get the gun out of the way, break that gun and throw it down the stairs, and then put him in a hold, throw him to the ground until the police came."
Jetstar said it was working with police and the airport to understand what happened.
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