Walking between Melbourne Central Station and the new Metro Tunnel State Library Station was initially going to count as a trip on the state's public transport network, attracting a myki card charge.
The Victorian state government declared there were no plans to intervene early on Wednesday but backflipped just hours later, opening the area up to everyone.
A government spokesman said a gate would be opened at the new station to create a "free thoroughfare" with rail network staff on hand to help passengers.
"These underpasses will be open to everyone with no Myki required," a Victorian Government spokesperson said.
The initial plan to charge pedestrians sparked backlash in the lead-up to the opening of the new $15 billion rail line, which will start taking passengers from Sunday.
A concourse connects the two CBD underground stations, allowing commuters to change between the Metro Tunnel and City Loop.
Two-hour full fares currently cost $5.50 and daily fares are capped at $11, with prices halved for concessions.
The charge would have prevented people from using State Library's Swanston Street entrance as a shortcut to and from Melbourne Central shopping centre.
In response to an outcry on social media, earlier Metro Tunnel sought to clarify that people did not need to touch on to visit the concourse - only the paid station areas.
"Entering any station and exiting at another is 'a trip' in the (Department of Transport and Planning) ticketing rules," it wrote on X.
"It's a free 'change of mind' to tap on and off at the same station within 15 minutes.
"If you've already touched on within the last two hours, on a train, tram or bus, you won't be charged for entering one station and leaving another."
Opposition public transport spokesman Sam Groth said it was effectively creating a pedestrian tollway.
"You'll be charged for taking a train you never took," he said.
"This doesn't happen in other states ... this needs to be simple for Victorians and make sure those people who decide to walk through, whether on purpose or inadvertently, aren't paying the price."
Spruiking the opening of a 120m-long pedestrian walkway under Anzac Station on Wednesday, Premier Jacinta Allan and Transport Infrastructure Gabrielle Williams were quizzed on the ticketing quirk.
Ms Williams refused to speak about the potential for future changes to rectify the issue.
She pointed out commuters transferring between the stations would not face an extra charge but recommended people travelling down from Swanston St to visit State Library go back out the way they came.
"I don't think it's that confusing an operation," Ms Williams said.
Ms Allan noted weekend public transport fares were being waived across Victoria from Sunday to February 1 to allow locals and tourists to familiarise themselves with the network.
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