The Melbourne-born former rapper was flown from Turkey to Darwin on a chartered flight on Friday morning ahead of a scheduled court appearance for extradition to Victoria.
Prakash was arrested and jailed in Turkey after allegedly flying to Syria to fight with Islamic State.
The 31-year-old is expected to face court in Darwin, where Australian Federal Police officers will apply to have him transferred to Victoria and charged with terrorism offences.
Prakash could face a life sentence if found guilty.
In 2016, he was wrongly thought to have been killed in a US military strike in the Iraqi city of Mosul, however later the same year Australian officials confirmed he was still alive and had been arrested in Turkey.
Former home affairs minister Peter Dutton revoked Prakash's citizenship in 2018 over his alleged ISIS participation and on the grounds he was Fijian.
Fijian immigration officials insisted Prakash, born to a Fijian father, had never held nor sought citizenship and refused to take him into the country.
Prakash rose to prominence over his alleged links to several terror plots in Australia and use of social media to lure potential recruits to Islamic State.
He was also listed in IS documents as one of the group's top recruiters
In a statement, the AFP said its officers maintained a thorough framework to manage Australians facing terrorism offences and there was no threat to the community.
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