The projects include a 22 turbine wind farm located at Sallachy and Duchally estate in central Sutherland and a 23 turbine wind farm situated at Glencassley Estate.
The wind farms were being developed German firm WKN Windkraft Nord and British energy company SSE, as reported by Bloomberg.
When considering the applications, the ministers concluded that the wind farms at Sallachy and the Glencassley will have an unacceptable impact on the Assynt – Coigach National Scenic Area (NSA) and the Reay-Cassley wild land area.
Energy Minster Fergus Ewing said: "The Scottish Government’s policy on wind farms strikes a careful balance between maximising Scotland’s huge green energy potential and protecting some of our most scenic landscape and wild land area.
"We have been clear that wind farms can only be built in the right places and Scottish Planning Policy sets out rigorous steps to ensure wind farms are sited appropriately and sensitively.
"I have considered these applications fully and recognise the efforts made by the applicants to mitigate the potential impacts of the Developments. However I have refused permission as the proposals would still have significant and unacceptable landscape and visual impacts in the local areas and these are not outweighed by any wider policy benefit."
In response to the refusal, WKN Windkraft said that the Sallachy wind farm have generated over 66MW of renewable energy.
It would also have attracted over £100m of inward investment and would have contributed £49m to Scotland’s economy.
The applications for Sallachy and Glencassley wind farms were submitted in 2011 and 2012 respectively.
