In an interview with Fox Business Network on Wednesday, Hughes said that he learned before the November 13 show that about six security guards at the historic venue had not showed up for work on the night that terrorist killed 89 people.
"It seems rather obvious they had a reason not to show up," he said.
On Friday, however, the singer and guitarist changed his tune on Facebook and Twitter, calling his assertions "unfounded and baseless."
"I humbly beg forgiveness from the people of France, the staff and security of the Bataclan, my fans, family, friends and anyone else hurt or offended by the absurd accusations I made in my Fox Business Network interview," he said in a statement.
"The shame is 100% mine. I've been dealing with nonstop nightmares and struggling through therapy to make sense of this tragedy and insanity. I haven't been myself since November 13. I realize there's no excuse for my words, but for what it's worth: I am sincerely sorry for having hurt, disrespected or accused anyone."
His comments on Fox came less than a month after Eagles of Death Metal returned to a Paris
stage to massive cheers. The sellout performance at the Olympia included 900 survivors and relatives of those killed at the Bataclan, which remains closed.
Hughes and the band had been playing at the Bataclan onstage for about an hour when three masked gunmen started shooting into the crowd with automatic weapons.
The November raid was one of a coordinated series of attacks on restaurants, cafes and venues -- including the Stade de France -- which left 130 people dead and scores more injured.
In a late November interview with Vice founder Shane Smith, band members praised the heroism
of their fans and recounted harrowing details of the attack and their eventual escape to safety.
"I want to be the first band to play in the Bataclan when it opens back up because I was there when it went silent for a minute," Hughes said in the interview.
CORRECTION: An earlier version of this story incorrectly identified the Fox Business Network.