The 17-year-old boy remains in custody after he was tackled down to the ground and arrested over the March 6 incident at Victoria's second-largest airport.
Police allege the boy climbed through a hole in a fence at Avalon Airport, near Geelong, before making his way on foot to the aircraft around 2.20pm.
About 160 passengers were on board the Jetstar plane, which was due to fly to Sydney.
The teen, who cannot be named for legal reasons, did not appear at a children's court hearing on Friday where the Commissioner of the Australian Federal Police applied for a suppression order.
It was revealed a joint counter-terrorism taskforce was involved in the investigation and the boy may have communicated with a foreigner or foreign entity over the March 6 incident.
Federal police successfully obtained a suppression on the identity of the foreigners, as well as the nature or content of the boy's communications.
The nature or contents of documents allegedly found in the accused's vehicle have also been suppressed.
The teen was originally charged with 12 Victorian offences but the court was told he is facing further federal charges.
The nature of those charges were not detailed in court or released to the media.
Police previously alleged the boy made bomb threats, placed a fake bomb and had stolen two shotguns and a rifle.
The teen allegedly stated "I've got bombs in my bag" and police claimed 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".
He is accused of placing a "faux homemade explosive", which was intended to look like it was legitimate.
The boy allegedly tried to "take or exercise control, whether direct or through another person" of the aircraft and is charged with stealing two 12-gauge shotguns and a rifle from a property in Tourello, north of Ballarat.
He is further charged with possessing cartridge ammunition and a registered category B long-arm without the appropriate licences, and being a learner driver who was driving unsupervised on Beach Road.
The boy is due to return to a children's court in April.
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