Testing was done after the ticks were found this spring in the three areas.
Morningside Park and the Rouge Valley are both located in the city's east end. Algonquin Island is part of the Toronto Island group of parks, across the harbour from the city's downtown.
The Blacklegged ticks can be found in tall grass and wooded areas and often latch on to campers and hikers, with potentially serious health effects.
They are not usually found in grass that has been mowed or in paved areas.
The ticks are the only type in Ontario that can transmit Lyme disease.
"Blacklegged ticks have recently been found in Toronto suggesting that these ticks are becoming established here," Public Health said in the statement Monday.
Health officials say the number of people with Lyme disease has gone up. In 2009 there were 128 cases in Canada. By 2013, that figure jumped to 682.
Experts say people should check for ticks after outdoor activities like walking the dog and mowing the lawn.
They also suggest wearing long sleeves and pants and other light-coloured clothing