Earlier this month, a Federal Court judge ruled that a portion of the law requiring would-be citizens to remove their face coverings while taking the oath of citizenship was unlawful.
Asked about the ruling last week, the prime minister denounced the court decision, saying most Canadians consider it offensive for someone to conceal their identity at the moment they are becoming a citizen.
But those in authority must be careful when treading on minority rights, said Trudeau, who said Harper's reasons for appealing the ruling aren't good enough.
"Any time a government or a leader is in a position to choose to limit minority rights of any type, there has to be a very good justification — a clear and compelling reason to do so," Trudeau said.
"The reason the prime minister gave last week for appealing the court's decision around the niqab was, to my mind, not at all justifying the prime minister's decision."
Zunera Ishaq, a Pakistani national, filed suit against the minister of citizenship and immigration, claiming the government's policy on veils violated the Canadian Charter of Rights and Freedoms.
The Islamic Supreme Council of Canada, a Calgary-based Muslim group, has called on the prime minister to reverse his plans to appeal.
The group says the Federal Court's decision to allow face coverings during citizenship ceremonies is "not an important issue," but that Harper is making it one unnecessarily.
It points out the identity of someone wearing a niqab during a citizenship ceremony can be verified by a judge before the oath is sworn.
The niqab is worn by some Muslim women in public areas and in front of men who are not relatives.
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