The Met Office has admitted its move from Bracknell to Exeter in 2003 went £7.9m over budget.
A Scottish Liberal Democrat MP raised the figure in the House of Commons over the future of the Aberdeen Met Office.
Malcolm Bruce is unhappy at the proposed closure and said he thinks the decision could have been taken partly because of the overspend.
The Met Office said the eventual cost was absorbed and had nothing to do with the proposed restructuring.
Mr Bruce said: "The Aberdeen office provides local coverage and I believe the customers will lose out by having it controlled from Exeter.
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We want to take advantage of that in the way we deliver services in the future
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"I have been told that the strategy to build the super centre at Exeter went over budget by £7.9m and I believe this could be one of the reasons behind the proposed closure of the stations.
Keith Groves, head of forecasting at the Met Office, said: "These changes are not linked to any impact of our relocation to Exeter.
"We now have a much more resilient infrastructure and clearly we want to take advantage of that in the way we deliver services in the future."
A 90-day consultation period over the stations' future was announced last week by Don Touhig, under-secretary of state for defence.
It allows for responses to be made to the consultation document which sets out four options as recommended by the Met Office board.
One option involves bringing together all non-military weather forecasts and some other services at the Exeter headquarters.