Marcel Blanchet has reversed an earlier decision and has now concluded Muslim women must remove their face coverings, or niqabs, when they vote.
Blanchet used special powers under electoral law to reverse the decision.
Elections Quebec had earlier decided that Muslim women will be allowed to wear the niqab, which leaves only a woman's eyes visible, if they sign a sworn statement attesting to their identity, show two pieces of identification and are accompanied by someone who can vouch for their identity.
Blanchet's initial decision prompted non-Muslim citizens to threaten they would show up at polling stations wearing masks.
After his announcement, Elections Quebec also received threatening phone calls and emails.
As a result, Blanchet had to get two bodyguards.
Quebec's three main political leaders had asked Blanchet to reverse the decision.
Liberal Leader Jean Charest requested on Thursday to have the decision reversed that would allow Muslim women to wear their niqab or burqa while casting their ballots.
Parti Quebecois Leader Andre Boisclair and Action democratique du Quebec Leader Mario Dumont agreed with Charest on the issue.
Boisclair said Elections Quebec has taken the hot-button topic of reasonable accommodation too far.
In recent months, Quebec has come under the spotlight for its treatment of reasonable accommodation for newcomers.
Sondos Abdelatif, 19, was given the ultimatum to withdraw from a corrections training session at a Montreal jail or remove her headscarf earlier this month.
In February, an 11-year-old Ottawa girl was ejected from a soccer game in Quebec after she refused to remove her headscarf during the game. The incident garnered international attention after soccer's governing body, FIFA, upheld the ban on headscarves.
Furthermore, the small town of Herouxville drew international attention when it adopted a declaration of "norms'' that outlines how immigrants must fit in.
With files from The Canadian Press