The 22-year-old jarred his left shoulder in a training drill this week in Queenstown.
He will head back to Melbourne for more treatment and assessment before his teammates return on Saturday.
"Given Arryn has completed most of the training camp, the club has undertaken a cautious approach by allowing him to return home and recuperate in Melbourne," St Kilda chief operating officer Ameet Bains told the club's website.
"He will be further assessed over the coming days."
Siposs had his second season in a row cut short by a shoulder injury this year and had the reconstruction after round 16.
He managed just three senior games for the year and had been struggling to maintain his form before the injury happened.
The 2012 NAB AFL Rising Star nominee is contracted until the end of next season, which shapes as a big one for him after just 28 senior games since he was drafted in 2010.
The Saints have been on their high performance camp since early last week and have undertaken a range of activities, including white water rafting, in between training sessions.
Most of the players are attending, but captain Nick Riewoldt has remained at home, following the birth of his first son James earlier this week.
The players taken in last week's rookie draft have been flown over to join their new teammates, with the exception of forward Ahmed Saad.
Saad has re-joined the Saints after serving his 18-month ban for testing positive to a banned substance and his suspension means he can't return to a professional sporting environment until the New Year.
