The MoD said it was concerned about a bid to build a windfarm at Minnygap Heights near Moffat due to the potential impact on a seismic station which monitors breaches of a nuclear test ban treaty.
Developers Renewable Energy Systems (RES) had bid to build 10 turbines at the site.
But the MoD said it could potentially interfere with their equipment at Eskdalemuir. The technology is sensitive to turbine noise and a tolerance limit for windfarms in the area has already been reached.
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RES described the Councillors’ decision as a "huge disappointment".
The wind farm had already been cut back by the firm from its original size of 15 turbines, but the renewed bid for the Annandale development has now been rejected.
Council planners also cited concerns regarding the impact of the windfarm on the landscape and tourism, when taken into consideration with a neighbouring 71-turbine development at Harestanes in Ae Forest.
Over 200 people objected to the scheme.
But RES says it is "confident" the turbines would not have been an issue for the seismic station.
RES development project manager Bruce Henry said: "Minnygap wind farm would have provided an efficient, reliable and sustainable way to supply clean energy for people living in Scotland.
"The wind farm would also have provided significant economic and social benefits for the local community in the form of a community benefit fund."
RES is considering its options following the decision.
(IT/CD)
