Two bodies were discovered at the site hours after a raging fire was brought under control at the building.
In total, 19 people were taken to hospital for treatment of injuries ranging from severe shock to extreme burns.
A spokesperson from the Sherbrooke University Hospital Centre said Friday morning that two people are still being treated for shock at their facility and four others were transferred to hospitals in Montreal.
Of those four, one person, a 42-year-old man, remains in critical condition with burns to 90 per cent of his body.
Cause of blast under investigation
The explosion happened at about 1:30 p.m. ET at Neptune Technologies et Bioressources Inc., located in the industrial area on Pépin Street.
The company makes health products from krill oil, which contains omega-3 fatty acids.
At a brief news conference Thursday evening, Neptune chief operating officer Michel Chartrand said the company is providing the appropriate support to its staff.
Chartrand said the company will continue to investigate the cause of the explosion with emergency services.
"All we're preoccupied with right now is our employees' well-being," said Chartrand. "Our next steps will be focused on them."
Fire followed explosion
The blast sparked a fire at the site and thick black smoke could be seen for kilometres.
Authorities say they were flooded with over a hundred calls within minutes of the explosion from people who heard the blast.
Firefighters arrived quickly and buildings surrounding the site were evacuated.
By 3:45 p.m., fire officials said the fire had been brought under control, but that they were still in emergency mode.
Police set up a large perimeter around the site and asked people to stay away while they kept searching the debris because of the risk of toxic exposure.
Environment Quebec said the toxicity concern stemmed from the plant's 15,000-litre acetone reserve, which was struck by the fire.
Acetone is flammable, and when ingested can cause irritation.
During a news conference Thursday evening, Dr. Marc-André Leclair said the fumes were not toxic and that everyone should be reassured.
Two dead found among rubble
Const. René Dubreuil, spokesman for the Sherbrooke police, said the bodies of two people were found Thursday afternoon when emergency workers were combing through the debris.
Hours later, another person was found in the wreckage, said Dubreuil.
"She was hiding in the debris and she was hiding because she was scared," said Dubreuil. "The person was found by firefighters when they made a search of the building to find people who were missing."
The injured were rushed to the Sherbrooke hospital, which issued a Code Orange and called all on-duty doctors to assist with in-coming patients.