Highland Council wants to close Edinbane, Dunvegan, Knockbreck and Struan primaries and construct a new school at Dunvegan on Skye.
Scottish ministers called in the proposal in May for consideration by a school closure review panel.
The panel said the council had not fulfilled its legal obligations.
Highland Council said it was disappointed by last month's decision. It was given 14 days to lodge an appeal.
The council argues there will be educational and community benefits as well as cost savings.
However, some parents objected, saying their children faced lengthy journeys to and from school.
Highland Council has lodged a summary application at Portree Sheriff Court seeking an appeal against the School Closure Review Panel's decision to refuse consent for a new community school in Dunvegan.
Drew Millar, chairman of the local authority's education, children and adult services committee, said: "The council believes that the panel has erred in its decision, which currently prevents us proceeding with the intended investment of up to Â£10m in a new community school.
"In pursuing this appeal the council believes it is in the best interests of the community, to provide new, state of the art facilities that will deliver first class, sustainable education into the future."
Highland Council has gone to court seeking to appeal against a decision refusing consent to the proposed closures of four schools on Skye.