Roberge said he had met with the young activist in France and discussed "access to education and international development".
The Canadian province of Quebec had just passed a law banning public sector employees from wearing religious symbols at work. This would include Malala Yousafzai's headscarf as seen in the picture.
The backlash was swift and came thick and fast.
"Nothing like having someone part of the suppression of education and work of minority Canadians posting a photo like this," one Twitter user wrote.
"Malala, what he fails to say is that his government just passed a law banning hijabi women from teaching in public schools, working as police or as judges. Shameful hypocrisy," another said.
But these replies were overshadowed by Roberge's own responses to a tweet, when asked by a journalist how he would respond if Yousafzai wanted to become a teacher in Quebec.
Roberge responded by voicing his support for the bill, saying it would be an "immense honour", but that in Quebec, as is the case in France and in other "open and tolerant countries", teachers can not wear religious symbols in their roles.
Bill 21 was passed in Quebec in June, which bars civil servants in positions of authority (including roles such as teachers, judges and police officers) from wearing religious symbols at work. This extends to symbols such as the kippah, turban or hijab.
Yousafzai became an honourary Canadian citizen in 2014 in Quebec, when Canada held the G7 summit, due to her campaigns on women and girls' health.
Yousafzai survived an assassination attempt by the Taliban as a teen and later founded the non-profit Malala Fund to help support a child's right to education. She became the youngest person to win the Nobel Peace Prize in 2014 when she was recognised for her global work supporting schooling for all children.