The government also plans to renovate an old dock and runway on Baffin Island, and use it to re-supply new Arctic patrol vessels.
Canada is at odds with Russia, Denmark, Norway and the US over 1.2 million square kilometres of the Arctic seabed, which a US geological survey estimates holds 25 per cent of the world's undiscovered oil and gas.
"In the Arctic, there are huge opportunities for diversified economic development, be we lack such obvious tools as shipping facilities"
Mary Simon, president of the Inuit Tapiriit Kanatami
As the polar icecaps melt, the region is becoming more accessible and by some estimates the Northwest Passage could open up to year-round shipping by 2050.
For the time being, though, the powers disputing the waters are only able to operate in them at certain times of the year.
Last month, Harper announced plans to build six to eight ice-breaking patrol ships at a cost of $7.1bn.
Canada currently has one large ice-breaker and five light-to-medium ice-breakers, "too few for the size of our Arctic," according to Robert Huebert, an Arctic geopolitical expert at Calgary University.
"It's about time that we're starting to take Arctic sovereignty seriously," he said.
The US has three aging ice-breakers, while Russia has just started building a new fleet of nuclear-powered ice-breakers.
Law and order
Canadian forces have operated in the Arctic since 1898, when a volunteer Yukon Field Force helped maintain law and order during the Gold Rush, but a modern military presence was only established in 1970, in Yellowknife, in Northwest Territories.
Less than 200 soldiers and 1,500 part-time Inuit rangers are now permanently based north of the 60th parallel, maintaining Canadian sovereignty over four million square kilometres.
Harper's announcement came at the end of a three-day visit to the North and prefaces a massive Canadian military exercise this weekend.
Meanwhile, locals demanded more attention be paid to the region's economy and help to reduce remote communities' reliance on costly air freight to import food and supplies.
"In the Arctic, there are huge opportunities for diversified economic development, be we lack such obvious tools as shipping facilities," said Mary Simon, president of the Inuit Tapiriit Kanatami, Canada's national Inuit organisation, in a letter to Nunatsiaq News.
The prime minister's visit to the North has been planned for months, but took on new importance after a Russia sent a submarine to the Arctic shelf and planted a Russian flag in a titanium capsule.
Meanwhile, Danish scientists are to head to the Arctic on Sunday seeking evidence to position Denmark in the race to claim the potentially vast oil and other resources of the North Pole region.
The monthlong Danish expedition will seek evidence that the Lomonosov Ridge, a 2000km underwater mountain range, is attached to the Danish territory of Greenland, making it a geological extension of the Arctic island.
That might allow the Nordic nation to stake a claim under a UN treaty that could stretch all the way the North Pole, although Canada and Russia also claim the ridge.