The quake was followed by a series of smaller aftershocks with the strongest registering 5.2, according to the agency.
The large aftershock struck within a few miles.
The US Geological Survey says a magnitude-6.2 quake has rattled the corner of British Columbia, near the boundary with Alaska.
"Incredible shaking felt in Whitehorse around 5:30 a.m. this morning", resident Jenni Beauregard said in an email to CBC.
The new tremor was registered at 14:18 GMT 84 kilometers (over 52 miles) northwest of U.S. city of Skagway.
No injuries or serious damage have been reported so far.
Many people in Whitehorse are in the dark.
Seismologist Taimi Mulder of the Geologic Survey of Canada tells CTV News Channel the quake occurred on the Fairweather Fault, also known as the Queen Charlotte Fault. On March 27, 1964 Alaska was natural disaster hit by the 9.2-magnitude quake, which one of the most powerful earthquakes ever recorded.
"We won't know until probably for the next week or two", she said.
The USGS says there have been a couple of aftershocks.