A young busker's venture to the big city took an unexpected turn when he inadvertently shut down a Melbourne train station after passengers mistook his didgeridoo for a gun.

Heavily-armed police swooped on Flagstaff Station and evacuated it about 8.30am on Thursday, with distressed passengers forced to rush from underground platforms.

Will Austin, from the central Victorian town of Daylesford, was searched by police as he headed out of the station carrying his didgeridoo in a black sleeve.

He was headed to Parliament station to conduct a workshop at the nearby Treasury Gardens, but hopped off at Flagstaff when the station was evacuated.

"I'm a country lad so I think I might have looked a bit suspicious," he told 3AW radio.

"I got stopped by police outside of Flagstaff station and searched, only to find that I didn't have a rifle."

It was reported passengers were alarmed when they saw the man carrying what looked like a gun and doing deep-breathing exercises, like he was meditating.

But Mr Austin denied he had been deep breathing.

"Although it was a big ordeal for nothing in the end, it was good to see the police had such a quick response and everyone can go home safe," he added.

Construction worker Shannon Marrell said he was rushed out of the station as heavily-armed police stormed onto the platform.

"I heard on the train that they had to duck, like they wanted everyone down," he told reporters.

Mr Marrell said a number of people appeared distressed when they had to rush out of the underground station.

Chief Commissioner Graham Ashton said the original report to police stated the man was carrying a rifle case.

"We're concerned there might've been someone with a firearm on a train this morning heading in towards the city loop," Mr Ashton told 3AW.

"We've stopped the train at Flagstaff and the critical incident response members conducted a search of the train and were after that ... content there was no firearm on the train, so they've given the all clear for those trains to resume."

Passenger Paddy Naughtin said he was on the 8.19am train to Mernda when it was stopped.

"A dozen cops came running past," he told AAP.

Mr Ashton said he would follow up reports a train driver had told passengers there was a gunman on the loose in the rail system.

"Oh dear ... we'll pick that up, if that's the case, and follow it up with Metro," he told 3AW.

"We have to be really careful about the sort of communications that are put out and when they're put out. You don't want people to be reacting in a way that might put their safety at risk."