The work to replace the track bed in the tunnel at Queen Street Station in Glasgow will close all platforms.
Network Rail confirmed the closure when asked about the work to rebuild the station and to electrify the Glasgow to Edinburgh line.
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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 Edinburgh-Glasgow Improvement Programme work could be done in days, not months.
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."
The work is needed as 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.
More details are expected to be available later this year.