"Obviously, this is every parent's worst nightmare," said Prime Minster Justin Trudeau.
Trudeau held a news conference in Davos, Switzerland, where he was attending the World Economic Summit, to announce the death toll in the remote northern aboriginal community of La Loche in the province of Saskatchewan.
Trudeau said five people had been killed and two others were in critical condition but a Royal Canadian Mounted Police spokeswoman later revised the death toll down to four.
The suspected shooter was taken into custody after police received an emergency call about "a person discharging a weapon in the community," RCMP superintendent Maureen Levy told reporters.
She said police were also investigating a second location in a nearby residential neighborhood, but provided no further details.
Authorities did not disclose the age and identify of the shooter and victims.
"We all grieve with and stand with the community of La Loche and all of Saskatchewan on this terrible tragic day," Trudeau said.
La Loche students said they heard six or seven shots ring out at around 1:00 p.m local time (1900 GMT).
Several witnesses reported seeing a "boy," who was either a student or formerly attended the school, opening fire inside the building.
"I ran outside the school," Noel Desjarlais, a Grade 10 student at the school, told public broadcaster CBC.
"There was lots of screaming. There was about six, seven shots before I got outside. I believe there was more shots by the time I did get out."
The town's hospital informed the media that they were treating the victims for gunshot wounds.
The high school and a nearby elementary school were locked down as police responded.
"It's just tragic and everybody's running around," said Kevin Janvier, acting mayor, adding that to his understanding the shooting took place when an individual walked in and "opened fire in the building."
Located deep in Canada's northern boreal forest, 600 kilometers north of Saskatoon, this town of about 3,000 is particularly isolated and authorities had to send in police reinforcements and dispatch a medical helicopter to airlift some victims to a hospital.
The school shooting is Canada's deadliest in 26 years.
On December 6, 1989, a 25-year-old man opened fire at the Polytechnic School in Montreal, killing 14 people, including 10 female students.
Unlike in the US, shootings are rare in Canada, where firearms are more regulated than south of the border.
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