But the rotating strikes are "a small price to pay" to protect smaller class sizes, teaching jobs and the rollout of full-day kindergarten, he said.
"The Elementary Teachers' Federation of Ontario has disrupted nine years of labour peace over a disagreement about pay," he said in a statement.
"It's regrettable that students miss any time learning, and it's unfortunate that families will need to make alternate arrangements."
Although the governing Liberals have the power to end the strikes, McGuinty said they won't intervene.
While he's disappointed that some teachers' unions have put students in the middle, McGuinty said he hopes teachers will take no more than one day away from school.
The government has said it has drawn up legal documents to stop any strikes that stretch beyond a single school day.
The premier argued that in the face of a $14.4-billion deficit, the province can't afford pay hikes for teachers.
But the union said the strikes aren't about pay, but a protest of a controversial new law that gives the government the power to stop strikes and impose a new collective agreement on teachers.
It's "unfortunate" that McGuinty "trivialized" the fight against Bill 115 as a disagreement over pay, said Sam Hammond, president of the Elementary Teachers' Federation of Ontario.
"The education sector's response to Bill 115 is not about a wage freeze or pause in salaries," he said in a statement.
"This strike action is about the government's unprecedented interference in the right to collectively bargain, a legal right provided for all people under Ontario law."
Elementary teachers in the Stratford and Timmins areas started the walkouts Monday, which are expected to spread across the province over the next few weeks.
On Tuesday, the strikes will move to the Niagara school board and the province's northwest Keewatin-Patricia board, while teachers in Ottawa-Carleton, Lakehead in Thunder Bay and Hastings-Prince Edward will walk out on Wednesday.
Elementary teachers in York Region, Trillium Lakelands in the Muskoka area and Renfrew say they'll walk off the job Thursday.
All elementary schools in the affected school boards will be closed the day of the strikes.
Teachers in the Toronto District School Board — the largest in Canada with about 550 schools — are in a legal strike position and started work-to-rule Monday, withdrawing from all administrative duties.
Fifteen other locals in Durham, Hamilton, Windsor and Peel regions — as well as two others in northwest Ontario serving areas in the Sudbury and Nipigon areas — have also started work-to-rule.
By Dec. 20, every school board in the province will have experienced a one-day strike, Hammond said.
"It is an inconvenience, but I say to parents this whole situation is regrettable," Hammond told CP24 from a union protest outside the Avon Maitland headquarters in Seaforth.
"I don't want to be doing this. The 75 members behind us here, my 76,000 members across the province do not want to be doing what they're doing."
Then the union should pay for the child care that parents are now scrambling to find for their kids, said Progressive Conservative education critic Lisa MacLeod.
"Thirty to fifty dollars is a lot to a lot of Ontario families," she said. "Especially those families who are going without this year because mom or dad doesn't have a job."
The Liberals can legislate teachers back to work, but they can't legislate goodwill, said NDP education critic Peter Tabuns.
"The minister could have a huge impact on the situation if she stood up and said: 'OK, I've learned ... we're going to scrap Bill 115, we're going to go back to the negotiating table'," he said.
Members of the Ontario Secondary School Teachers' Federation withdrew Monday from all non-classroom work, including extra-curricular sports and events such as holiday concerts.
Hundreds of high-school students walked out of class Monday in protest of the legislation, including at least two Toronto schools and one in Parry Sound.
"I'm just really glad that a lot of people are actually just exercising their right to have a voice, because with Bill 115, they're legislating the teachers back to work," Catherine McArton, who organized the walkout at Parry Sound High School, told radio station CKLP.
"They're taking away their democratic right. So we're going to exercise ours."
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