Police claim the 17-year-old climbed through a hole in a fence at Victoria's second busiest airport and made his way to the aircraft where he allegedly told those on board he was carrying explosives.
The incident took place on a Jetstar plane due to fly from Avalon Airport, near Geelong, to Sydney with 160 passengers on board on Thursday afternoon.
The teenager has been charged with multiple offences including unlawfully taking control of an aircraft, orchestrating a bomb hoax and possessing a firearm.
The boy, who cannot be named for legal reasons faced a children's court on Friday and will remain custody until his next appearance on March 21.
According to court documents released after the hearing, he allegedly said: "I've got bombs in my bag".
Police allege it could be inferred his intention was to "destroy, damage or endanger the safety of the aircraft or kill or injure all or any of the persons on board".
Police also allege he had two stolen shotguns and a rifle.
Neither Victoria Police nor Australian Federal Police have a stationed presence at the airport.
The Transport Workers Union has called for a security review of Australia's airports, pushing for a co-ordinated safety approach across the country.
"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," union national secretary Michael Kaine said.
Flight Attendants Association Australia federal secretary Teri O'Toole was concerned that someone could enter restricted areas of the airport, including while planes are parked overnight.
Ms O'Toole praised the crew's bravery, noting that Jetstar had offered them support.
"As the last line of defence, they came through," she told AAP.
Avlaw Aviation Consulting chair Ron Bartsch described the incident as "simply not acceptable".
"It makes a mockery of having sophisticated scanning and security systems if people can simply bypass it," he told ABC Radio.
Avalon Airport chief executive Ari Suss said the organisation has set up more security measures, including within the terminal and the surrounds.
Victoria Police crime squad investigators are working with Australian Federal Police counter-terrorism personnel in the probe.Â
The teen allegedly tried to climb the front stairs into the plane cabin but was subsequently overpowered by three civilians.
"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," Victoria Police Superintendent Michael Reid 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 ABC.
"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."
Mr Clark was flying to Sydney with his friends - the parents of Sydney Swans star Jake Lloyd - to celebrate the AFL player's 250th game against Geelong on Friday.
The veteran Swan offered his thoughts to everyone on board during the terrifying situation.
"It sounds like there were some incredibly brave actions from Barry and others to keep everyone safe," Lloyd said in a statement.
"I'm grateful that my parents are OK."
Jetstar chief executive Stephanie Tully praised the pilot and cabin manager who helped apprehend the teen.
"They're trained to do this, but it doesn't stop these efforts being heroic," she said.
Avalon Airport has fully reopened and flights are operating as normal.
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