Couillard warned Fatima Houda-Pepin on Friday to fall into line and not to make any declarations outside the caucus.
He also said she will have to follow the party line if a vote is held on the controversial charter, which would ban public sector workers from wearing obvious religious symbols such as the hijab on the job.
On Thursday, Houda-Pepin wrote a letter to The Canadian Press saying she was "shocked" by colleague Marc Tanguay when he said he would welcome candidates wearing the chador and would be happy to sit beside them in the legislature.
The chador is an open cloak which extends over the head but does not cover the face. It is worn by many Iranian women.
Houda-Pepin, who was born in Morocco, said she has long been concerned about the rise of fundamentalism while staying silent on the Liberals' position, which opposes any ban on religious symbols as long as the face is uncovered.
She said Thursday she rejects "any drift toward cultural relativism, under the guise of religion, to legitimize a symbol like the chador, which is the ultimate expression of oppression of women, in addition to being the symbol of radical fundamentalism."
Her remarks might not sway any votes in the legislature where the Parti Quebecois minority government does not have enough support to pass its plan.
However, the Parti Quebecois has threatened to make the charter a confidence issue and campaign on it if if the government falls. Houda-Pepin's remarks would likely then be used against the Liberals.
Coulllard also had stern words for Tanguay, saying he would not accept any candidate wearing a chador.