Fortin, 40, will sit as an Independent until the 2015 federal election.
"The Bloc Quebecois in which I believed, which we believed, no longer exists," he said in a statement.
"The arrival of new leader Mario Beaulieu, who is pushing a one-dimensional, unrigorous and uncompromising approach, has put an end to the credibility established by Gilles Duceppe and continued by Daniel Paille, two leaders who deserved great respect."
After a summer of reflection, Fortin said he believes his constituents would be better served if he completed his mandate outside the party, which will now have only three MPs.
Beaulieu has made no bones about focusing on the promotion of sovereignty — an approach that differs from that of his predecessors.
Beaulieu, who is on a provincewide tour to drum up support for independence, has accused Duceppe and Paille of having a defeatist attitude with regard to sovereignty.
The party leader downplayed Fortin's harsh criticism, suggesting the MP showed disloyalty to the party and the sovereigntist cause.
"He (Fortin) lacked loyalty and transparency," Beaulieu told a news conference. "He never accepted the democratic decision of Bloc Quebecois members."
Beaulieu went further, saying Fortin had a "hidden agenda" and had planned to form a new party. Beaulieu said party officials intercepted an email about one month ago outlining such a plan.
The leader said Fortin's departure comes after numerous discussions, including one on Monday. There was no mention of him quitting the party, Beaulieu said.
Beaulieu said Fortin's actions, just a year away from a federal election, amount to "jumping ship and torpedoing the independentist cause."
Fortin has represented Haute-Gaspesie-La Mitis-Matane-Matapedia since 2011. A political scientist and former municipal politician, he did not indicate if he would seek re-election next year.
Fortin says Beaulieu has radicalized the party with his dogmatic approach.
"It is not by rejecting those who seem less 'pure' and abandoning the rigour which has always characterized the Bloc in favour of repeating old...formulas that he will convince Quebecers to follow him," Fortin said.
"This is not the way to serve Quebecers or advance sovereignty. In behaving this way, Mr. Beaulieu is dividing sovereigntists instead of uniting them."
Beaulieu flatly denied the notion of division within the party, insisting that everyone else in the Bloc family is on the same page.
His departure leaves leadership runner-up Andre Bellavance, Claude Patry and Louis Plamondon as the party's only MPs.
The Bloc has been in turmoil since its staggering defeat at the polls in 2011, when it was reduced to four seats from 47.
Fortin ran for the party leadership in 2011 and lost to Paille.
The runner-up in that race, Maria Mourani, was expelled from the Bloc caucus in September 2013 by Paille for criticizing the Parti Quebecois's now-defunct proposed charter of values.
She has since been sitting as an Independent and has denounced sovereignty.
Paille quit as leader in December 2013 because of health reasons, with Beaulieu replacing him this past June.
— With files from Stephanie Marin in Ottawa
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