A photo of Marc Tanguay, the logo of the national assembly and his contact information appeared on the website of the FATH community centre.
Couillard called for the ad to be withdrawn, saying public funds should not have been used.
"It's not a question of freedom of expression," he told reporters as he continued his economic mission in France.
"Freedom of expression allows people to say stupidities and that's why it exists."
But the Quebec premier said public funds should not be used to help spread such opinions.
Couillard suggested Tanguay may not have been aware of the hateful comments when the ad was placed.
Tanguay removed the ad after the premier's remarks.
The Montreal-area Muslim community centre describes itself as a non-profit association whose services include the teaching of the Qur'an and language courses for children and adults.
Its virtual library includes books which openly encourage violence against women.
One book says if a wife does not say her prayers or refuses to obey her husband's orders, he should take her to task...and even "go as far as to strike the woman, although it should not be painful."
On Tuesday, Tanguay refused to remove the ad and said in a statement he advertises with other organizations in his riding.
He also said the community centre did not commit any illegal acts.
But the opposition said Wednesday that Tanguay had committed a regrettable error, with the Parti Quebecois demanding he apologize for downplaying violence against women.
It's not the first time that Tanguay has found himself at the centre of a religious controversy.
During an interview with The Canadian Press in 2013, he said he was ready to welcome Liberal candidates who wore the chador, a piece of dark clothing worn by Muslim women that covers the body and leaves only the face exposed.
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