In May 2006, he attracted a number of complaints after an appearance on the Quebec television show Tout le monde en parle in which he stated that at his age he enjoyed defecation more than sexual intercourse.
In September 2006, Fournier penned a piece for the Quebec magazine 7 jours in which he sought to make a point about treatment of homosexuals in Lebanon, which included the line:
In Lebanon, the law makes it possible for men to have sexual intercourse with animals as long as they are females. To do the same thing with male animals could lead to the death penalty.
Following extremely negative public reaction to these remarks, he appeared on Tout le monde en parle to apologize and indicate he would refrain from writing for 7 jours in the future and instead concentrate on his CBC duties. However, several more days of news coverage followed, which also focused on his previous comments about defecation.
On 19 September 2006, Fournier resigned from his position as CBC chairman which was accepted by Heritages Minister Bev Oda.  Members of Parliament applauded Fournier's decision to step down - Independent MP André Arthur being the only one known MP to denounce his resignation.