The Trust stated that the decision, which was announced by Scottish energy minister Fergus Ewing on June 6, was made without a local public inquiry.
The conservation charity added that written objections to the Stronelairg windfarm outnumbered supporting letters by a margin of almost 15 to 1.
John Hutchison, chairman of the Trust said: “Over the past year, the Scottish Government has made ground-breaking progress by adopting the new Wild Land Areas map of Scotland, and, for the first time, recognising wild land as an important national asset.
“However, we believe the decision by the energy minister to give the go-ahead to Stronelairg without a Public Local Inquiry is not consistent with Scottish Government measures to protect the best areas of wild land from industrialisation.”
He added that “because of the scale of the development” a Public Local Inquiry should be completed.
When granting approval in June, Ewing said the windfarm would help “keep the lights on across our islands at a time where there is an increasingly tight gap between electricity supply and demand”.
He added that the development would create jobs both in its construction, and during its lifetime, as well as benefitting the local community “through the provision of a Sustainable Development Fund.”
Ewing also stated that the Scottish Government wants to “see the right developments in the right places”.