He is now being interviewed in relation to the offences of Acts in Preparation to Commit a Terrorist Attack and Collecting Documents to Facilitate a Terrorist Act, contrary to the Commonwealth Criminal Code Act.
Police said Tuesday that Ali Ali, an Australian born to Somali parents, sought to target Federation Square in the city center, one of the most popular spots to spend the annual celebration in the city.
Police released footage of the arrest on Tuesday.
According to charge sheets Mr Shire acted "in preparation for, or planning a terrorist act" between March 31 and April 6.
He was taken into custody by the Special Operations Group police just before 3pm in Werribee.
"The allegations are that he was planning to commit a terrorist act and that he attempted to obtain a gun to do so", Victoria Police Deputy Commissioner Shane Patton said.
"What we will be alleging is that he was intending to use a firearm to shoot and kill as many people as he could in Federation Square area on New Year's Eve".
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"Absolutely police were aware of this very early and had been monitoring", she said.
There is no ongoing threat to the public, police said.
The perpetrator may face a life term in prison.
That property is still being searched by police while his place of work, a computer business in Footscray, and a relative's home in Meadow Heights are no longer being searched after warrants were executed at those locations on Monday.
Police have charged 74 persons in counter-terrorism investigations since 2014.
"I can absolutely assure Victorians that this has eliminated the risk", she said.
The 20-year-old was allegedly connected to Australian jihadist circles including other terror suspects and extremist preacher Junaid Thorne.