The huge simulation exercise involved 650 land, sea, air and special forces members and is part of Operation Nanook 12's month-long training exercise. The annual operation in the North gives the Canadian Forces a chance to practice their skills in responding to emergency and security situations.
Harper was aboard the HMCS St. John's to observe Operation Nanook 12 along with Defence Minister Peter MacKay and Gen. Walt Natynczyk, chief of defence staff.
Afterward, Harper addressed Canadian Forces personnel in a speech aboard HMCS St. John's, and reiterated some of the themes of his northern tour.
"In an uncertain world, where demand for resources is growing, where any number of civilian needs can suddenly come upon us, and where conflicts and potential conflicts remain ever present, you, our men and women in uniform, are here to literally stand on guard for the True North strong and free," Harper said.
"And it tested your response to an entirely plausible threat, that of ships entering our waters illegally. It involved all elements of the Canadian Armed Forces," Harper said of the simulated exercise.
"And as I watched the interception and storming of the 'vessel of interest' earlier today, I was deeply impressed, and frankly, as a Canadian, I was unabashedly proud of the skill and precision with which you performed."
This operation has been taking place in the Eastern Arctic, in the Hudson Strait, and in Hudson Bay near Churchill, Man., where Harper watched today's exercises.
Another scenario is taking place in the Western Arctic in and around Inuvik and Tsiigehtchic, Northwest Territories. That practice situation involves land and air forces.
This year's Nanook operation began Aug. 1, and with 1,250 personnel involved in total, it's the biggest one yet. The cost for the entire operation is $16.5 million.
Exercises anticipate threats
"Both scenarios will underline the domestic role played by the Canadian Forces in safeguarding the nation, deterring threats to our security, and responding to emergencies in the High North," the department of national defence said in a news release when Nanook 12 began earlier in the month.
The Canadian Coast Guard, the Royal Canadian Mounted Police, local officials and officials from Public Safety are all involved in the operation.
The scenario Harper watched mirrors the situations experienced in British Columbia in recent years where boats carrying Tamil migrants arrived. The Conservative government has promised to crack down on human smuggling and has made several reforms to the refugee system.
Friday is the final day of the prime minister's trip to the North.