The rock band were mid-performance on 13 November when four Islamist militants shot and killed 90 fans.
Hughes apologised on Facebook for his comments on Fox News last week about six security guards who were not at work on the night of the attack.
He said he made "absurd accusations".
Speaking to Fox News on Wednesday, Hughes said he had learned that some guards did not come to work that night and "it seems rather obvious that they had a reason not to show up."
The owners of the Bataclan were quick to dispute this, saying he had made "grave and defamatory accusations".
Their statement said that a judicial investigation was under way and that "we wish to let justice proceed serenely".
"All the testimonies gathered to this day demonstrate the professionalism and courage of the security agents who were on the ground on November 13. Hundreds of people were saved thanks to (these agents') intervention," they added.
Hughes responded on Friday, saying: "I humbly beg forgiveness from the people of France, the staff and security of the Bataclan, my fans, my family, friends and anyone else hurt or offended by the absurd accusations I made in my Fox Business Channel interview."
He said his comments were "unfounded and baseless" and that he had been struggling with dealing with the trauma of the massacre. The raid on the concert was one of seven co-ordinated attacks across Paris, killing 130 people. 'I haven't been myself''
"I've been dealing with non-stop nightmares and struggling through therapy to make sense of this tragedy and insanity," he said.
"I haven't been myself since November 13. I realise there's no excuse for my words, but for what it's worth: I am sincerely sorry for having hurt, disrespected or accused anyone."
The Californian rock band escaped the carnage by hiding in a dressing room backstage and later told how they wanted to return to Paris to finish their performance.
They returned to Paris three months later to finish the gig at another venue, the Olympia, after receiving "overwhelming" support.
The Bataclan survivors were all invited and many attended amid tight security. The show included a silence in memory of the victims.