At a magnitude of 6.2, the temblor hit northwest of Mosquito Lake, a hamlet with a population of about 300.
Residents in Whitehorse have reported power outages and minor damage, but detailed information about damage and possible injuries was not immediately available.
There are no reports about damages and victims.
A series of moderate earthquakes rocked Juneau awake early Monday morning, but no significant damage was reported and no tsunami warning was issued. Natural Resources Canada estimated the depth of the quake at 10 kilometres. "Was in bed and woken up by violent shaking".
Vaughan said the area is highly seismic and a quake of this magnitude isn't unexpected.
Ruppert said the biggest aftershock recorded so far was a magnitude 4.7.
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Heath Scott, chief of police in Haines, about 60 miles (96.5 kilometers) southeast of the quake epicenter, said it shook a picture frame off his file cabinet.
Earlier in the day, the area was hit by a 6.2-magnitude quake.
Powerful earthquakes nearly always spawn aftershocks that can continue for years, she said, adding that the level of seismic activity in the Haida Gwaii region of B.C. remains elevated, five years after a magnitude 7.8 quake there.
Vaughan said the shallow initial quake had the potential to cause damage but the remote location dropped the chances of major problems.
According to a number of witness testimonies, the quake was felt in city of Whitehorse, the largest city in northern Canada and the only city in the Yukon.
The U.S. Geological Survey reports several other earthquakes in the area at around the same time, including one that measured 5.2.