The Sustainable Development Commission (SDC) warned of a discrepancy between national aims and local decisions in an assessment of the Scottish Government's progress.
It said the draft national planning framework aligns with sustainable economic growth but questioned how it will cut greenhouse gases. It also raised fears on rail links planned to support airport growth, claiming that ministers lack robust data on aviation's cost and benefits.
However, it praised the ministers' work on the Scottish Climate Change Bill, a draft of which is due before parliament next month.
Scottish environment secretary Richard Lochhead responded: "This bill will set the most ambitious targets anywhere in the world. There remain a number of challenges to face and we will continue to work with the SDC."