The regulator found mining company Baffinland's plans did not conform with the territory's land use plan, CBC reported.
Baffinland wanted to triple the amount of ore shipped from Milne Inlet to 12m tonnes per year, bringing in ships for 10 months of the year, rather than just in the summer.
Icebreakers would be needed to allow bulkers in and out.
Hunter Tootoo, the commission's chair, said: "In the plan there's essential areas which are harvesting areas and community transportation routes.
