The 51-year-old, who was jailed in 2016 after being convicted of inviting support for the Islamic State terror group, was taken from the high security Belmarsh prison in south-east London early on Friday morning, the Press Association understands.
Once a leading figure in the now-banned group al-Muhajiroun, the former solicitor had previously stayed on the right side of the law for years.
Choudary was due for automatic release after reaching the halfway point of a five-and-a-half-year sentence, when time spent on remand is taken into account.
For the rest of the sentence period, he will be subject to a strict supervision regime.
Police and MI5 are expected to be among a host of agencies involved in monitoring him in the community.
It is thought he will initially be placed in a probation hostel and will have to comply with more than 20 licence conditions.
There are a number of standard requirements, including maintaining good behaviour, receiving visits from and keeping in contact with his supervising probation officer, and not travelling outside the UK without prior permission.
In addition, Choudary will be subject to a bespoke package of further measures while on licence.
These are expected to include: electronic tagging; a night-time curfew; requirements to stay within a set area and only attend pre-approved mosques; a ban on contacting individuals who he knows or believes to have been charged with or convicted of extremist-related offences without prior approval; and restrictions relating to internet use and mobile device ownership.
Any breach of licence conditions can result in immediate return to custody.
Choudary, from Ilford, east London, will be supervised under a system known as multi-agency public protection arrangements (Mappa).
In a separate measure, his name has been added to a UN sanctions list, which means he is subject to an assets freeze and travel ban.
On Thursday, Theresa May said authorities are equipped to supervise Choudary after his release.