Planning permission for the scheme was overturned earlier this month after the Court of Session ruled that the public were not given the opportunity to comment on the revised application, and an objection from Scottish Natural Heritage had not been taken into account.
The development was approved by Scottish energy minister Fergus Ewing in June 2014.
However, charity the John Muir Trust challenged Ewing’s decision to approve the wind farm without any public local inquiry and lodged a petition to the Court of Session asking for a judicial review.
Announcing the decision to challenge the Court of Session ruling, a Scottish Government spokesman said: "Scottish ministers have considered the judgement of Lord Jones in relation to the petition lodged by The John Muir Trust for the judicial review of the Scottish ministers’ decision to grant consent to construct and operate the Stronelairg wind farm, Garrogie Estate, Fort Augustus.
"Scottish ministers are appealing the decision."
