The work, to replace the track bed in the tunnel, which is the only way in and out of the high-level station, will close all seven platforms.
Network Rail confirmed the closure when asked questions about the work to rebuild the station and to electrify the Glasgow to Edinburgh line.
The work is not related to either the redevelopment or the electrification, but is expected to take place in two years time.
It comes months after rail bosses ruled out a lengthy closure of the station, saying the EGIP work could be done in days, not months.
In September, Network Rail told the Evening Times: "We have no plans to close Queen Street Station for up to 12 months. While we are still evaluating options for the EGIP works at the station, a long-term closure is not among them."
Rail bosses said contingency plans will be put in place, using the two low level platforms, Central Station and other stations in the city to minimise disruption to passengers.
Transport Minister Keith Brown was asked about potential closures due the Queen Street redevelopment but he would only say that disruption was inevitable and it was ultimately a matter for Network Rail.
The Evening Times asked Network Rail a series of questions relating to potential disruption during the works and was told of the separate maintenance programme.
A spokesman for Network Rail said: "The redevelopment and associated electrification works will not require a long-term closure of the station.
"There is a separate project to renew the slab-track within the Queen Street tunnel which will impact on services and will likely be delivered in 2016.
"This work is a long-standing, planned investment and was mentioned in our strategic business plan published last year.
"It could require the closure of the tunnel for around three to four months."
The work is needed as, over the years, water ingress in the tunnel has eroded the track deck.
During the closure services that currently come into Queen Street High Level, including the Edinburgh, Aberdeen and Oban trains, as well as services from Stirling and Alloa via Lenzie and to Anniesland in the west will be disrupted.
The two low-level platforms are currently busy with services to and from Helensburgh, Milngavie, Balloch, Airdrie, Edinburgh and Springburn.
Contingency plans will be drawn up and more details are expected to be available later this year.
The separate work on redeveloping Queen Street, revealed yesterday in the Evening Times, will take place between 2016 and 2019 one platform at a time, meaning potentially less disruption but reducing the capacity at the station from seven to six platforms.
There has been concern that the first service to be cancelled during this period is one to Anniesland, with fears it could be temporarily withdrawn or the service significantly reduced during the work.
The Network Rail spokesman said: "The work will require us to close one platform at a time to complete the extension of them.
"This will require a reduction in the number of services using the high-level station and the diversion of some to the low level.
"We are still assessing which services this will affect and how long for."
Nicola Sturgeon, Deputy First Minister, has previously given a commitment that as long as the SNP is in government the service and stations on the Anniesland line are safe, and Transport Minister Keith Brown said disruption would be minimised.
He said: "There is going to be some disruption but we will be looking to minimise it.
"People understand there will be some disruption to complete this work."
He was unable to say if there would be closures, stating it was a matter for Network Rail.
However, he said there will be restricted access at certain times when demolition work and rebuilding was being carried out.
He said: "There was major refurbishment work at Haymarket Station in Edinburgh, which did not require closure."
The work on renewing the tunnel is not part of EGIP or the Station plan but part of Network Rail's business review for work between April and March 2019.
Network Rail said it was contracted to deliver the scheme for £104m by 2019 and did not expect the cost or timescale to change.