The guidelines partly reflect efforts by the Trudeau government to fashion Canada as a liberal progressive model on issues including immigration and health care policy. Mr. Trudeau has been an outspoken proponent of women and their reproductive rights.
The Liberal government’s stance is a marked contrast to that of the Trump administration, which last year cut off federal funding to Planned Parenthood and other groups that perform abortions, a move that conservatives applauded. In the same year, the Trudeau government pledged to spend $650 million on sexual and reproductive health and rights.
On Friday, the Toronto Right to Life Association said it had applied to the Calgary offices of the Canadian Federal Court for an order to at least temporarily invalidate the job-application guidelines.
The group said Friday that it had sued the Ministry of Employment in the same court earlier this month, asserting that the guidelines violated the Canadian Charter of Rights and Freedoms, which, the group said, guarantees freedom of expression, conscience and religion.
Blaise Alleyne, the organization’s president, said by phone from Toronto that he was shocked that the Canadian government had imposed its views on Canadians and penalized groups for upholding their religious beliefs.
He warned that the policy could lead to staff shortages at soup kitchens, shelters, summer camps and small businesses that had received funding from the program, while denying young people work experience.
“Trudeau has politicized a program that up to now was just supposed to be about summer jobs,” Mr. Alleyne said. “In a free and democratic society, you should be able to disagree with the government and not be disqualified because you don’t share Justin Trudeau’s beliefs.”
Earlier this week, on “Fox and Friends,” Rachel Campos-Duffy said the policy appeared calculated to “silence pro-lifers” in Canada.
“This is a sign of intolerance,” she said. “If you have a pro-life view you’re not welcome to share it or else you’re kicked out of this program.”
Groups that support abortion rights suggested that conservatives had twisted the intent of the policy, but acknowledged that the wording was unclear.
On Friday, Joyce Arthur, executive director of the Abortion Rights Coalition of Canada, said the policy had been meant to ensure that the government would not be funding groups that undermine human rights. But she said the lack of clarity had allowed the policy to be hijacked by conservative groups pressing their own ideological agendas.
“It was a no-brainer requirement,” she said by phone from Vancouver. “But the wording needs clarification so the issue doesn’t get misunderstood. Unfortunately, it has become a big distraction.”
The Conservative opposition leader Andrew Scheer accused Mr. Trudeau this month of using the requirement to impose his own views on Canadians. Speaking at a meeting hosted by the Mississauga Board of Trade, he said community groups were expressing alarm that they would be unable to employ youths and provide services because of their beliefs. Among the groups affected was the Southern Alberta Bible Camp, which told CBC News, the Canadian broadcaster, that it would lose about $40,000 for six summer counselor positions.
Mr. Trudeau, who has sought to balance his own Roman Catholic religious views with his commitment to abortion rights, has called the reaction to the policy a “kerfuffle.”
Both he and the employment minister, Patty Hajdu, have stressed that the policy was not intended to target religious groups.
Speaking at a town-hall meeting in Hamilton, Ontario, last week, Mr. Trudeau affirmed that Canadians were entitled to their beliefs. But he added: “When those beliefs lead to actions determined to restrict a woman’s right to control her own body, that’s where I, and I think we, draw the line as a country. And that’s where we stand on that.”
In 1988, Canada’s Supreme Court struck down the country’s then restrictive abortion law, which allowed only abortions approved by hospital committees. It said the law was unconstitutional and interfered with a woman’s right to control her own body.
The decision came after an abortion clinic operator, Dr. Henry Morgentaler, had asked the Supreme Court to overturn an Ontario appeals court’s ruling that he undergo a trial on charges of conspiring to perform illegal abortions.
David Millard Haskell, an associate professor of religion and culture at Wilfrid Laurier University in Waterloo, Ontario, said the Supreme Court had left it for the federal government to introduce new legislation on the issue but successive governments on both sides of the ideological spectrum had avoided it, fearing they would polarize the country.
Because no replacement law was introduced, legal experts and human rights advocates said, Canada has no legal restriction against abortion, which, they said, was at the discretion of patients and their doctors.
Since the Morgentaler decision, abortions have been publicly funded under the Canada Health Act, for both hospitals and clinics.