Hughes' band were playing at the venue on the night when Islamist terrorists killed 130 people in attacks across Paris, including 90 at the gig.
In an interview with Vice shortly after the attack, Hughes said he wanted to be the first person to play at the Bataclan when it reopened. However, Hughes and his manager were turned away from the venue last night, according to the manager, Jules Frutos.
Speaking to the Press Association, Frutos said: "They came, I threw them out — there are things you can't forgive.
"They tried to enter the venue and they are persona non grata. They are not welcome after what he said about the security."
Hughes, who Frutos said did not have a ticket for the event, previously suggested that Bataclan's security guards had helped the terrorists.
Hughes, a Republican, said that six of the venue's security guards had not shown up on that night and that it seemed "obvious" they had "reason not to show up". In an interview with "libertarian webzine" Taki's Magazine, Hughes also claimed to have seen Muslims celebrating on the streets after the attack in an interview.
Although Hughes later apologised for his comments, which he called "absurd accusations" and said were "baseless", Frutos said of Hughes: "Even if he came back on what he said. I mean, this man is just sick."
However, speaking to Billboard music website, the Eagles of Death Metal band manager Marc Pollack claimed no such incident had occurred and lambasted Frutos for spreading "mean-spirited words of hate".
Pollack said: "This day is not about Jesse Hughes or Eagles of Death Metal.
"In fact, Jesse is in Paris to share in remembering the tragic events of a year ago with his friends, family and fans.
"This is about recalling the tragic loss of life that happened right in front of his eyes during his show and this coward Jules Frutos feels the need to soil his own club's reopening by spreading false tales to the press."
At the concert last night, the proceeds of which will be donated to charities supporting families of victims, Sting opened with the song Fragile, about the fragility of humanity and includes the lyrics: "Nothing comes from violence and nothing ever could."