Earlier this month the Evening Times revealed the upper level station would shut for 16 weeks in 2016 to allow work to renew the track bed in the station tunnel.
The work is separate from the redevelopment of the station, to be completed by 2019, and the electrification of the line between Glasgow and Edinburgh.
Sandra White, Kelvin SNP MSP, asked the minister in the Scottish Parliament about the closure and why local businesses were not informed of the plan and what measures would be put in place to deal with disruption.
She said it was: "An announcement that was not conveyed to Glasgow Chamber of Commerce or any local businesses.
"Can the minister tell me what if any contingency plans have been made for users of Queen Street Station and will there be a consultation and who will be involved."
Mr Brown said: "It's important to be clear that the closure Network Rail referred to is not part of the Edinburgh to Glasgow Improvement Programme (EGIP), rather it's related to the renewal of the existing track bed in the Queen Street tunnel.
"We would certainly want to have further discussions with Network Rail on that point.
"A disruption management forum is to be convened by Transport Scotland involving stakeholders such as tasked with minimising any disruption to the travelling public."