The press advert, which ran last December, links Scottish First Minister Alex Salmond's support for wind farms to his backing of the release of Lockerbie bomber Abdelbaset al-Megrahi for humane reasons.
Trump has been campaigning to stop the development of the Vattenfall-led 100MW European Offshore Wind Deployment Centre, which will be located near his luxury golf course and hotel.
Lang Banks, director of environmental charity WWF Scotland, said: "When it comes to wind power, Donald Trump's grasp of the facts has once again been shown to be totally lacking. The advert was pretty distasteful, and it's now been shown to be factually wrong, too."
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