Police say the 17-year-old climbed through a hole in a fence at Victoria's second busiest airport before making his way on foot to the aircraft.
The incident took place on a Jetstar plane due to fly from Avalon Airport, near Geelong, to Sydney with 150 passengers on board on Thursday afternoon.
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 and faced Victoria's Children's Court on Friday morning.
Avalon Airport has fully reopened with all flights operating as normal.
The Transport Workers' Union has called for a security review of Australian airports, pushing for a Safe and Secure Skies Commission to ensure a coordinated safety approach across the nation.
"There are serious questions to be answered here," the union's National Secretary Michael Kaine said.
"We need to see all players working together towards a safer and better aviation industry instead of relentlessly cutting costs, which has seen safety plummet at our airports."
Flight Attendants' Association Australia federal secretary Teri O'Toole was concerned that someone would have been able to enter restricted areas of the airport, including while planes are parked overnight.
Ms O'Toole praised the bravery of the crew and said Jetstar had offered them support.
"This is a perfect example of, as the last line of defence they came through."
Avlaw Aviation Consulting chair Ron Bartsch described the incident as "simply not acceptable".
"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 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.
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, Victoria Police Superintendent Michael 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.
