The apology came a day after police and the Toronto District School Board said they were investigating complaints about the material, which was posted on the East End Madrassah's website. The school has since removed it.
The material should never have been part of its curriculum and a team of scholars is reviewing all texts and materials, the school said in a release.
"Our curriculum is not intended to promote hatred towards any individual or group of people, rather the children are taught to respect and value other faiths, beliefs and to uphold Canada's basic values of decency and tolerance," it said.
"We unreservedly apologize to the Jewish community for the unintentional offence that the item has caused."
Premier Dalton McGuinty weighed in on the controversy Tuesday, saying he's pleased both police and the Toronto District School Board were investigating whether the school was promoting hatred.
"There is no room for hatred or intolerance in this province," said McGuinty, who is expected to meet with Israeli President Shimon Peres on Wednesday.
The complaint came from the Friends of the Simon Wiesenthal Centre, which found the material on the school's website and alerted the school that it had lodged a complaint.
The Centre for Israel and Jewish Affairs denounced the material as "offensive and abhorrent."
"Such slurs against the Jewish community violate the values that Canadians hold dear, such as goodwill and mutual respect," Sheldon Goodman, the centre's Greater Toronto co-chairman, said in a statement.
"Instead of promoting such values, this curriculum only serves to promote animosity, racism and hatred."
The school has a permit from the school board to teach lessons on Sunday from rented space in a public school in the city's east end.
The centre said the board should more carefully scrutinize who rents its space and take a closer look at what's being taught on its property.
Progressive Conservative Leader Tim Hudak urged the minister of education to work with police to investigate the complaints and "prosecute this to the fullest extent of the law."
"Israel has no greater friend than Canada," Hudak said. "I'm proud of that and our province should be in the exact same position."
The school's apology isn't good enough, he added.
"It's not a matter of reviewing materials," Hudak said. "This is hatred. This is poison. This type of material has no place in our classrooms, no place in the province."