Armed and masked police have arrested two people as part of a counter-terrorism operation near an inner-Melbourne Anglican church.

Video footage on Friday showed a handcuffed man in a white forensic jumpsuit being led from near St Mary’s Church in North Melbourne to a waiting vehicle. A woman was also cuffed and arrested, according to reports.

BREAKING: Melbourne's Joint Counter Terrorism Team have just arrested a man next to St Mary's church in North Melbourne @9NewsMelb pic.twitter.com/LWXS3FK6kk — Carrie Greenbank (@CGreenbank9) April 26, 2019

Police also attended a block of apartments in Bedford Street in North Melbourne, about 300m away from the St Mary’s church, with two officers guarding the front door on Friday night.

It is understood they carried out a search warrant at the apartment complex, seizing a number of items from the building.

Victoria police were tightlipped about the operation, while the federal police also would only confirm the involvement of the joint counter-terrorism team.

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

“We can hear a few helicopters,” the worker said. “We drove through before, it was all blocked off, the road. Police [are] everywhere.”

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

A resident, named as Sara, told the Herald Sun that she heard the police arresting the man.

“I heard them yell ‘get down on the ground’,” she said. “I looked out the window and saw the man on the ground with police in camouflage gear sort of on top of him.

“The police had these huge assault rifles and it looked really serious.”

Sara said she saw police put the man into a white plastic suit.

“I didn’t hear sirens or see lights or anything, and the wasn’t yelling or screaming or resisting arrest,” she said. “There was very little commotion.”

ABC News Breakfast presenter Virginia Trioli was passing by and said the weapons being held by the officers “looked like they came out of Avengers: Infinity War”.

“They were pointing a man on the ground and there was a woman who was on the opposite corner who was down on the ground with a security person overlooking her as well,” Trioli told the ABC.

She said a witness at the scene had told her the man was holding a backpack at arm’s length and officers had screamed at him to drop it.

Victoria police confirmed the joint counter-terrorism team was tasked to a job in North Melbourne on Friday afternoon, and two people were assisting with inquiries.

A Victoria police spokeswoman said there was “no current or impending threat to the community”.