Separately, the US military also scrambled fighter jets in Montana to investigate a radar anomaly that triggered a brief federal closure of airspace.
"Those aircraft did not identify any object to correlate the radar hits," the North American Aerospace Defense Command (NORAD) said in a statement.
Canadian Prime Minister Justin Trudeau first announced Saturday's shootdown over the northern Yukon territory, saying Canadian forces would recover and analyze the wreckage of an unidentified cylindrical object.
Canadian Defence Minister Anita Anand declined to speculate about the origin of the object, which she said was cylindrical in shape. She stopped short of calling it a balloon but said it was smaller than the Chinese balloon shot down off South Carolina's coast a week ago, though similar in appearance.
Aloft at 40,000 feet (12,200 m), it posed a risk to civilian air traffic and was shot down at 3:41 EST (2041 GMT), she added.
"There is no reason to believe that the impact of the object in Canadian territory is of any public concern," Anand told a news conference.
US fighter jets from Joint Base Elmendorf-Richardson, Alaska, monitored the object as it crossed over into Canadian airspace, where Canadian CF-18 and CP-140 aircraft joined the formation.
"A US F-22 shot down the object in Canadian territory, using an AIM 9X missile following close co-ordination between US and Canadian authorities," Pentagon spokesman Brig. Gen. Patrick Ryder said in a statement.
US President Joe Biden authorized the U.S. military to work with Canada to take down the high-altitude craft after a call between Biden and Trudeau, the Pentagon said.
The White House said Biden and Trudeau agreed to continue close coordination to "defend our airspace."
"The leaders discussed the importance of recovering the object in order to determine more details on its purpose or origin," it said in a statement.