There was never just one government in Alaska during territorial days. In fact, the Secretary of the Interior under President Woodrow Wilson identified a "government of the forests, a government of the fisheries, one of the reindeer and Natives, another of the cables and telegraphs" and listed several more before he finished adding them up.
His comments reflected the reality that the real governing power in Alaska was not the weak territorial government, which could not tax or regulate fishing, mining, and other major economic activities. It was really the unelected officials from the federal agencies that controlled Alaska affairs. Until statehood, 99% of the land was under federal control. There were nine federal departments with as many as 38 bureaus operating in Alaska. The federal agencies managed land that they controlled, often without considering any local concerns. This created ongoing controversy in Alaska, where the people thought their views should be given more weight.
Current Federal Lands in Alaska
While the situation has changed considerably since Alaska's territorial period, the federal government continues to own the majority of Alaskan land today.
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