"We will have a crew going out to clean up the provincial park beaches in this area,” said John Cooper, a ministry spokesman based in Peterborough, Ont.
Initial estimates pegged the number of dead waterfowl as high as 6,000, but Cooper said ministry staff were going to do an updated assessment on Monday.
Tests were being done to determine the cause of the deaths, but previous such die-offs often were caused by the waterfowl eating botulism-laced fish, Cooper said.
"It’s not uncommon to have these kind of die-offs of fish and birds on the Great Lakes at this time of year, but in this location and this number is unusual."
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The die-offs along a roughly three kilometre stretch on Georgian Bay is the largest Ontario officials have seen in many years. About a decade ago some 25,000 birds died on Lake Erie from eating botulism-laced fish.
The government clean-up will centre on a large provincial park on the shores of southeast Georgian Bay, but private landowners in the area near Wasaga Beach will be left to their own devices, Cooper said.
"They can leave the carcasses there and let nature take its course, they can bury the carcasses on the property or they bag them up and put them out with ... the garbage," he said Sunday in a phone interview.
It was unclear if more birds would wash ashore, but Cooper said it was possible the problem would persist for several weeks.
"I would hope we’re peaking right now but in previous situations the factors are water temperature and wind directions but it could linger on for another month or so but I would think the bulk of the event is happening now."
Botulism toxins are easily destroyed by heat, meaning fish and birds that people catch pose no risk provided they're properly cooked, Cooper said.
However residents in the area are being warned to keep a tight rein on their pets and prevent them from getting near the dead birds and fish on the beaches.