The site in Broadford will be a 'hub' facility for the area and include a community hospital and resource centre; while an additional 'spoke' facility will be constructed in Portree.
Shona Robison, Health Secretary, will now be asked to approve the board's proposals.
Garry Coutts, Chair of NHS Highland, has described the decision as "historic" and said detailed planning for the new facilities would now begin.
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He said: "We have reached a crucial stage in the redesign of services in the area. Our public engagement and consultation has been both lengthy and thorough, and we are satisfied that we have reached a decision that best reflects the needs and aspirations of the entire community. I am delighted to recommend it to the Cabinet Secretary.
"Understandably, there has been some controversy around this issue. People have approached it from various perspectives, and our job has been to try to arrive at a consensus view on how best to reshape our services.
"We have done so with the interests of the entire community at heart and would ask everyone in Skye, Lochalsh and South West Ross to pull together behind this decision."
The proposals have been opposed by some of the community living in the north of the isle who have said they would prefer the main hub facility to be developed at Portree.
(JP/IT)
