The public will not see any change under the proposal to cut the number from eight to three across Scotland, Roseanna Cunningham told MSPs.
She defended the plan after claims from Labour and Liberal Democrats that it amounts to a cut in frontline services.
She said: "The public will not see any change.
"When an emergency call comes in, the same appliance will be sent out from, most likely, exactly the same fire station as previously, with the possible exception of the improved service that will come from there no longer being boundaries."
Five different IT services across the control rooms makes it "almost impossible" to work as a single unit at present, she said. The Scottish Fire and Rescue Service board agreed last month to scale back an original plan to close six control rooms, keeping three open instead.
Only Scotland's busiest control room - at Johnstone in Renfrewshire - is certain to stay open. It handles about half of all calls.
Aberdeen, Inverness, Dundee and Edinburgh are in the running for the other two places.
Control rooms at Dumfries, Thornton in Fife and Maddiston near Falkirk will not be considered.
Lewis Macdonald, a Labour MSP for the North East, said 1200 people signed an online petition to save the control room in Aberdeen.
"Many people in the north-east agree with the Fire Brigade Union that neither the highly-trained control room staff nor anyone else has been properly consulted on the scale of these cuts to frontline services," he said.
Sarah Boyack, Labour MSP for Lothian region, wanted reassurances about the Edinburgh control room. "I recently met with the staff in Tolcross fire station and was very struck by the regional knowledge, not just the local knowledge that they have from across Lothian and the Borders."
North East Liberal Democrat MSP Alison McInnes pressed the minister. "The staff taking 999 calls in control rooms across Scotland are delivering a frontline service," she said.