The ruling is the second time Norrbotten has foiled Jokkmok Iron Mines AB's ambitions for the site and furthermore recommended that the Mining Inspectorate confirms the decision in order to protect reindeer herding in the area.
"We believe that the haulage roads will affect the area much more than the mine itself. It concerns in many cases virgin territory where the plans are for road or rail," county governor Sven-Erik Österberg told local media.
The plans for the Kallak mine have faced strong protests and demonstrators in 2013 tried to prevent the company's exploratory drilling operations by blocking the road and chaining themselves to vehicles and other objects. Some also climbed up in trees around blasting site.
The issue is set to remained unresolved for the time being however as even if the Mining Inspectorate backs up the board's decision, the company retains the right to appeal.
Sweden's Samis, part of the 80,000 strong Nordic indigenous peoples who inhabit a huge swathe of land stretching from Norway across Sweden and Finland to Russia, have for centuries moved their reindeer down from the snow-covered mountains for lowland grazing.
The mining industry is one of several modern threats to the unique way of life of the Samis and when residents of the Jaahkaagasska area near the subarctic town of Jokkmokk got wind of the plans for Kallak they decided to fight back.
Jokkmokk Iron Mines CEO Fred Boman has previously claimed that the fears were exaggerated and expressed confidence that the mine would be approved by the government.
"This is a very solid and large ore find and the economic value of this weighs more than the local reindeer herding business," he told AFP as the protests raged late last year.
"But (reindeer herding) has important cultural value, and we are absolutely convinced that we can get on with this together."
According to advocates for the mine, the Kallak project would bring some 500 jobs for at least 14 years to Jokkmokk, a town numbering only 5,000 citizens.