Consortium Veridis Energy, led by Irish Recycling Services, had planned to build the facility on the Ballyutoag Road, situated between north Belfast and Nutts Corner.
Verdis are said to be "deeply disappointed" with the decision, which was supported by MLAs, and are beginning the appeal process.
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A letter from Northern Ireland's Environment Minister Edwin Poots to MLAs said: "The planning service has recommended this application be refused and I concur with this advice."
Alastair Nicol, Engineering Development Manager with Veridis, said: "Solving the problem of our energy dependency is not as simple as sticking up a few wind turbines,
"In due course, we will need every source of energy to survive. Delivering energy from waste is an essential part of that.
"We believe in the value and quality of this project and that people will soon realise the pressing need for it."
Northern Ireland is required to vastly reduce the amount of waste it sends to landfill in-line with strict EU targets.
(GK/BMcC)
