Mulcair said he is not against women wearing the full Islamic veil at oath-taking ceremonies or employees displaying it in the federal civil service.
Conflicts over religious clothing are the domain of judges and its not up to politicians to interpret the Canadian Charter of Rights and Freedoms, he said.
"Freedom of religion is guaranteed under the charter," he said. "It's up to the courts to set parameters and to decide limits."
Prime Minister Stephen Harper has said the government will appeal a recent Federal Court ruling allowing people to take citizenship oaths with their faces covered.
Harper said Canadians are overwhelmingly against people wearing the niqab at citizenship ceremonies.
One of Mulcair's MPs from Quebec, Alexandre Boulerice, said last week he was uncomfortable with federal bureaucrats wearing niqabs in the workplace.
Mulcair said Tuesday that Boulerice was only expressing a personal opinion and not representing the party's position.
ALSO ON HUFFPOST: