The study by the lobby group People for Education released Monday also found that some were getting physical activity on alternate days, but no children in Toronto were getting the full mandatory dose of daily activity.
"There was a study done of kids in the GTA where they put [a] special kind of pedometers on them and found that in fact, none of them, were getting the full 20 minutes a day," Annie Kidder, the executive director of the lobby group, said on CBC's Metro Morning.
Even this bare minimum is below the recommended amount, Kidder told host Matt Galloway.
"That's not, according to Canadian health standards, what kids are supposed to be getting every day," she said.
The report, funded by the Heart and Stroke Foundation and based on surveys from 1,000 Ontario schools, also found that 45 per cent of elementary schools have a specialist health and physical education teacher, and the majority are part time.
However, the GTA fared better on this measure — 75 per cent of all elementary schools had a health and physical education specialist on staff.
Principals say not enough time, training
Kidder said that many principals who responded to their survey say it is difficult to incorporate physical activity into the school day.
"Because it's mandatory, principals when they respond to our survey say, 'Yes, we're delivering it.' But what they also say is, 'It's very hard, there's not enough time in the day. Teachers aren't trained enough, and they're having a hard time fitting it in," Kidder said.
Emily Fisher, a health and physical education teacher, told CBC News the curriculum was "heavy" but physical activity is important for students.
"There's a lot to get done during the year and during the day," she said. "But the teachers do make it a priority to get their kids up and moving."
Madhura Kumar told CBC News her seven-year-old daughter is getting some good exercise with her gym teacher, but it's not enough.
"That way, I'm happy, but I would like to see my daughter getting physical education every day rather than probably every alternate day," she said.
More attention needed on children's health, professor says
Kidder says the Ministry of Education needs to create a clear strategy for student health and well-being.
"A lot of evidence that says schools are the place to do something about not just physical health, but health writ large," he said.
The province should set goals for children's physical health the same way it has set standards for education in English and math, Kidder said.
"We've seen in Ontario great strides made in reading writing and math... Those are the goals you hear over and over, to get the scores up in reading, writing and math. What we haven't done is set the same kind of goal in terms of health and well-being."
John Freeman, an associate professor in the faculty of education at Queen's University, agrees with Kidder.
"I think we have to give the same kind of attention to health as we currently give to literacy and numeracy in this country, and that's across the country," he told CBC News.
"Until we start saying that health is important, and so important that we want to make sure it's improved and make sure we're going to assess how its improved … we're not going to have these kinds of changes."