Police are yet to reveal what prompted armed and masked officers to zero in on two people at North Melbourne on Friday afternoon.
A handcuffed man in a white forensic jumpsuit was seen in video footage on Friday being led from nearby St Mary's Church in North Melbourne to a waiting vehicle.
A woman was also cuffed and arrested, according to reports.
Police described the incident as a "routine operation".
"This operation is not linked to a specific incident and is part of the Joint Counter Terrorism Team's ongoing intelligence gathering. It is also not linked to any imminent threat," a police statement on Friday night stated.
Police arrested the pair, who were being questioned on Friday night.
Officers also raided a nearby block of apartments in Bedford Street in North Melbourne.
The Joint Counter Terrorism Team comprises members of Victoria Police and the Australian Federal Police, which said there was no threat to the community.
