Hicks, dubbed the "Australian Taliban" in Australian media, was taken directly to Yatala prison by a police convoy.
David McLeod, his lawyer, said Hicks was "elated" to be returning to Australia but that there were fears for his mental health after spending years in Guantanamo Bay.
"In the western world's most notorious prison, he's become institutionalised," Mcleod said.
McLeod said security at Guantanamo was at "fever pitch" on Hicks's departure and the former kangaroo skinner was restrained in his seat during the 24-hour flight via Tahiti.
Australia's government defended the $413,000 cost of bringing Hicks home.
|Hicks supported the Taliban during the early stages of the US liberation of Afghanistan|
Alexander Downer, the foreign minister, said Hicks was unable to fly commercially "because of the security issues".
A small group of protesters outside the jail carried placards in support of Hicks.
But Downer said he should not be treated as a hero.
"You are dealing with somebody who is a criminal here and somebody who has been involved in several terrorist organisations, in particular, al Qaeda," he said.
The 31-year-old is the first terrorist suspect to be convicted by a US military commission in Cuba.
He will be placed in the high-security G-division at Yatala, alongside Australia's worst serial killers, a gang of four who murdered 11 people and disposed of several bodies in barrels hidden in a disused bank vault.
McLeod said Hicks wanted to put the past behind him and would respect a US gag stopping him from speaking to the media for a year after his March conviction.
"He wants to get on with his education and, if possible, go to university," McLeod said.
"He's not proud of his notoriety and he simply wants to get on and move on."
Hicks, a convert to Islam, confessed to receiving training from al-Qaeda fighters in Afghanistan prior to the September 11 attacks on New York and Washington in 2001.
As part of a plea-bargain with US prosecutors he admitted to one count of giving material support for terrorists and agreed to co-operate with US investigators.
In return, the US government gave him a seven-year jail sentence - much of which he had already served - and agreed to let him complete a portion of the sentence in Australia.
His military attorney, Major Michael Mori, portrayed Hicks as an apologetic soldier wannabe who never shot at anyone and ran away when he got a taste of battle.
Prosecutors however said that Hicks freely joined a band of killers who slaughtered innocent people.