About a dozen people who had symptoms of gastrointestinal illnesses were treated by paramedics at the fair Tuesday night and five of them were sent to hospital.
By 9 p.m. Wednesday dozens more cases were reported, bringing the total to nearly 100.
A spokeswoman for Toronto Public Health said the agency is focusing its investigation on Epic Burger and Waffles — a food vendor known for its headline-making cronut burger, which uses a croissant-donut hybrid as its bun.
"However, all possible sources of illness are being investigated," Dr. Lisa Berger said in a statement.
She added that "overall risk to the general public is low."
Epic Burger and Waffles released a statement Thursday saying they would voluntarily remain closed for the second day in a row as the investigation continues. But the company stood by its record.
"In the time that we've been operating at the CNE we have had a clean bill of health and all our staff have been fully trained in food safety," the company wrote.
"We buy our products from only the top suppliers and we've never had any issues in the past, nor do we wish to have any in the future. We take health and safety very seriously."
Toronto Public Health has said people reported feeling sick after consuming food between Aug. 16 and 20. Berger added that samples of food were sent to a laboratory for testing, and it typically takes between 48 and 72 hours to get results.
Public health has not confirmed the source of illness.
"All the food that was available at that food premise has been disposed of," Berger said at a news conference Wednesday.
People could have become ill at the fair due to dehydration and heat as well as food, she said.
Public health is asking anyone with symptoms such as an upset stomach, diarrhoea, fever, vomiting, stomach cramps and dehydration to notify the organization.
Prior to the exhibition, Berger said more than 1,600 food handlers had been trained and public health officials did more than 200 inspections at the site.
Toronto Mayor Rob Ford said he feels for the people who got sick.
"It's terrible when people have diarrhea and are vomiting all night," he said. "You get food poisoning — it is the worst — I've had it a couple of times and you just feel like you're dying."
However, Ford said he believes the issue has been resolved and encouraged people to go to the fair and "have fun."
CNE general manager David Bednar said Thursday that the reported illnesses don't appear to have affected attendance at the fair, but noted that it might be too early to tell.
"Sometime people are a little bit slow to react to these things and we won't really know if there's been much of an impact, if any, until a few days have gone by," he said.
The CNE remains open until Sept. 2.