Five investigators on Tuesday morning were digging through what was once the back of the food court, at times employing an excavator to move the rubble.
The team also used hand shovels and a rake to meticulously sort through the debris in some sections.
"The investigation has led us to the southeast corner of the building itself. We're doing an excavation in there, examining all the fire patterns," said supervising investigator Lonnie Schubert.
"There's things like chip vendors, pizza I believe. As you can imagine, there's a number of electrical appliances We have to look at all those things. Everything is a potential ignition source until we can eliminate it."
Investigators have yet to rule out any possible causes, including foul play, he said.
Meanwhile, the owner of the market said its outdoor section would be open on Thursday morning as it is every week.
"We're going to have to move some of the outdoor vendors to different locations because [the fencing] takes up a bit of area," Marcus Shantz, head of the company that owns the building, told The Morning Edition host Craig Norris on Tuesday morning.
Firefighters were first notified of the blaze at the 24,000-square-foot building, which was made almost entirely out of wood, just before 2 a.m. Monday. There were no sprinklers installed in the building — that was not a construction requirement when it was built more than 20 years ago.
Damage is estimated at more than $2 million.
The market is a popular southern Ontario tourist destination and a prominent local landmark.