He is accused over a plot to disrupt a major defence conference at Canberra's Hyatt Hotel on Wednesday, when rocks were hurled through a window during the navy chief's speech.
Police are still to provide further detail on the device it says was thrown.
It was seized by the AFP bomb squad and continues to undergo forensic examination.
The accused 20-year-old was arrested in Canberra on Friday and charged with damaging property.
Both offences carry a maximum 10 years' imprisonment.
The ACT Joint Counter Terrorism Team investigated the incident alongside the Australian Federal Police and ASIO.
"Police will allege the incident was intended to cause panic and fear among attendees of a conference being held at the hotel," according to a statement issued on Saturday.
Various other items were seized during police raids at homes in the Canberra suburbs of Campbell and Scullin on Friday and are undergoing forensic investigation, police say.
Further charges haven't been ruled out as detectives continue investigations into the possible involvement of others, AFP assistant commissioner Stephen Nutt said.
"Let me be clear, this was not a prank," he said.
"This was an extremely dangerous act we allege was intended to, and did, have a chilling effect on conference attendees, as well as staff and other guests of the hotel.
"We will not tolerate criminal behaviour or actions which advocate hatred, fear, violence and humiliation, and attempt to erode Australia's social fabric."
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