The ceremony at Rideau Hall is the latest in a series of events marking the 200th anniversary of the war.
Harper presented the medals and flags to representatives of 48 native communities with ties to the war.
He says First Nations and Metis warrior fought alongside English and French-speaking militias and British regulars to repel American invaders in the 1812-14 conflict.
More than 10,000 native fighters participated in almost every major battle of the campaign.
Without their help, Harper says, history might have been different.
"The commemorative medals and banners being presented today recognize the vital contributions and enormous sacrifice made by our First Nations and Metis peoples during the War of 1812," he said during the ceremony.
"Without their courage and honour, Canada would not have been able to successfully defend itself and we would not have the peaceful and prosperous country our citizens enjoy today."
Aboriginal Affairs Minister John Duncan and Gen. Walter Natynczyk, chief of the defence staff also took part in the ceremony.