Australian Federal Police (AFP) charged the man with four counts of making a document likely to facilitate terrorist acts.
The man has spent the day in hospital after complaining of abdominal pain and he is due to appear in Melbourne Magistrates Court later on Thursday.
The man, from Officer about 50km southeast of Melbourne's CBD, was arrested on Wednesday following a series of raids on 11 properties that allegedly uncovered guns and extremist propaganda.
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One of the properties targeted during the raids was the Al-Furqan Islamic Information Centre in Springvale, which Muslim leaders said was on the fringes of the Muslim community.
But members at the centre had reported how they exposed who they believed to be an undercover police officer about three weeks before the raids occurred.
Text messages the man had written were posted online by the group while leaders from the centre expressed their shock at being watched so closely.
