Quebec Premier Philippe Couillard called the decision "disturbing," while the Canadian Civil Liberties Association deemed it troubling, discriminatory and a violation of the Canadian Charter right to freedom of religion.
Justin Trudeau declared it to be "just plain wrong."
On Tuesday, Quebec Court Judge Eliana Marengo told Rania El-Alloul inside a Montreal courtroom she had to remove her hijab before the court would hear her case against the province's automobile insurance board, which had seized her vehicle.
Marengo said that she wanted her courtroom to be secular and El-Alloul's Islamic headscarf was inappropriate.
El-Alloul refused to remove her hijab, and in response, Marengo suspended the case indefinitely.
On Friday, a spokesperson for the Prime Minister's Office said "if someone is not covering their face, we believe they should be allowed to testify."
The Liberal leader weighed in during an event in Montreal.
"The fact that in this situation, in a courtroom of all places, someone's fundamental rights weren't respected is absolutely unacceptable and we expect that there will be consequences," Trudeau said.
NDP Leader Tom Mulcair said the judge made a mistake.
"I expect this individual to be given a full and proper hearing in short order," Mulcair told reporters in Toronto. "It's a simple matter of that person's rights as a Canadian."
A spokeswoman for the Court of Quebec said Friday it is standing by Marengo's decision and the judge would not bow to public pressure.
Annie-Claude Bergeron repeated Friday that judges are masters of their courtroom and have the right to interpret the law and set the rules of the court as they see fit.
El-Alloul did not return messages from The Canadian Press, but told CTV News on Friday that she is planning to file complaint.
"It's my right, I'm Canadian," she said.
Couillard said that in his government's opinion, the only time one should be required to remove an article of religious clothing is if it creates problems for "communication, identification or security."
"I will be very careful because the judge is sovereign in her decisions, in her courtroom," Couillard told reporters in Quebec City. "I'm a little bit disturbed by this event, I must say."
Sukania Pillay, the Canadian Civil Liberties Association's executive director, said the state has no right to be in people's closets and to tell women what to wear.
"The courtroom has every right to be secular," said Pillay. "But that doesn't translate into telling people what they can and cannot wear in a manner that's incompatible with their freedom of religion."
Lucie Lamarche, a lawyer and a spokeswoman for Quebec's league for rights and freedoms, said there is "no judicial precedent" for Marengo's decision.
"The judge has the right to enforce the decorum in the courtroom," Lamarche said. "But there is no definition of decorum."
She said Marengo's decision was "extremely personal and discriminatory regarding what it means to be dressed properly in the courtroom."
Lamarche added that the chief justice of the Court of Quebec has the ability to remove a judge from a particular case and that El-Alloul can make that request.
Stephane Beaulac, law professor at Universite de Montreal, said Marengo's decision was a "blatant violation of the woman's fundamental rights and freedom."
El-Alloul exercising her freedom of religion by wearing a hijab was not incompatible with the judge hearing her case, he said.
Beaulac said that El-Alloul can file a complaint with the body that oversees judicial conduct in Quebec, called the Conseil de la magistrature.
"This judge will need to face the music," Beaulac said.
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