Video footage on Friday showed a handcuffed man in a white forensic jumpsuit 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.

A man who walked near the church during the operation said he saw men wearing masks and carrying "machine guns", believed to be police.

"Detectives from the Melbourne Joint Counter Terrorism Team conducted a routine operation in North Melbourne this afternoon," a police statement on Friday night states.

"This operation is not linked to a specific incident and is part of the JCTT's ongoing intelligence gathering. It is also not linked to any imminent threat."

Two people are being questioned by police.

A worker at nearby business Trutrack Suspension said the police action seemed to focus on the church.

"We can hear a few helicopters. We drove through before, it was all blocked off, the road. Police (are) everywhere," the worker told AAP on Friday afternoon.

International tourists were allegedly locked inside their accommodation until it was safe to leave, Nine News Melbourne reported.

"He was handcuffed, and he was just waiting with the military guy next to him, and then the police arrived," an unnamed witness told the network.

Another witness said she saw "(police) wearing camouflage and it was really weird because they had guns".

Police 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, and there is no ongoing risk due to the operation.

Australian Associated Press