But Couillard was reluctant to say outright whether he disagreed with the decision.
"I will be very careful because the judge is sovereign in her decisions, in her courtroom," Couillard told reporters Friday in Quebec City.
"I am a little bit disturbed by this event I must say."
Couillard said an infringement on religious freedom is only justified in certain situations, such as when an individual needs to be identified or security is an issue.
On Thursday, CBC News reported that Judge Eliana Marengo told a woman in a Montreal courtroom she would not hear her case until she removed her hijab.
Rania El-Alloul was in court to apply to get her car back after it was seized by Quebec's automobile insurance board, the SAAQ, because her son had been driving with a suspended licence.
The incident has sparked widespread discussion across Canada and especially in Quebec, where the province has had a heated debate about secularism and the limits of reasonable accommodation.
Mulcair, Trudeau critical of judge
Opposition Leader Tom Mulcair said El-Alloul should have been allowed to plead her case while wearing a headscarf.
"It's a simple matter of that person's rights as a Canadian," he said.
Liberal Leader Justin Trudeau also weighed in, calling the incident unacceptable.
"All Canadians deserve to have their rights protected, especially in a court of law," he said on Twitter. "Let's remember who we are."
Haroun Bouazzi, co-president of the Association of Muslims and Arabs for a Secular Quebec, said the judge doesn't understand the concept of a religiously neutral state.
"This woman has been penalized because of her belief, which makes the state not neutral anymore," Bouazzi said.
Bouazzi's organization has reached out to El-Halloul to help her file a formal complaint against the judge.
A spokesperson for the chief judge of the Quebec Court said judges have "a lot of discretion to interpret the law as they see it."
Judge Marengo did not respond to requests for comment.