"I want to be perfectly clear about this: training materials that portray Islam as a religion of violence or with a tendency towards violence are wrong, they are offensive, and they are contrary to everything that this president, this attorney general and Department of Justice stands for," Holton said. "They will not be tolerated."
The training materials, Holton said, "pose a significant threat to national security, because they play into the false narrative propagated by terrorists that the United States is at war with Islam."
Holton said that he spoke about the issue with Holder directly when he was out in Oregon.
"He is firmly committed to making sure that this is over," Holton said. "Now the reality is it is going to take a bit to go back and figure out what trainings have happened in the past that we need to go back and fix -- we're a big organization, we've got lots going on with lots of people and lots of contractors -- but Attorney General Holder is firmly committed to it, and we're going to fix it."
Assistant Attorney General Thomas Perez also condemned the anti-Muslim training material in his subsequent speech during a conference on anti-Muslim discrimination, saying that Muslims have "every right to be upset about the issue of the trainings."
"The Attorney General is equally upset, the Deputy Attorney General is upset, the FBI Director is upset, and we're upset because we have accomplished so much," Perez said.
"I recognize the words of my mother, that it only takes one or two incidents to make all that great work seem a part of the past," Perez said. "So we have to make sure that we have the quality control across the board."
Holton struck a similar theme, recalling how he talked to his local FBI special agent in charge (SAC) the day after the Quantico revelations came out.
"The SAC said to me -- Greg Fowler, who used to be in New York, he's now in Oregon -- said 'You know, they tell you on your first day as an agent at the FBI that one person can make a difference. What they forget to tell you is that it can be a good difference or a bad difference.' So we're working hard to get that right," Holton said.
Progress has been made on engagement with Muslim communities, including in the way that criminal complaints refer to Islam, said Holton.
"Before this effort, a lot of us didn't understand that when we make an arrest in a high-profile terrorism case that involves someone who claims they follow Islam, it creates a mini-backlash against people in communities," Holton said.
"In the 37-page complaint that laid out the allegations against Mohamed Mohamud, he is never once identified as a Muslim. We were very careful about that. It's not relevant from our perspective, what's relevant is the violence," Holton said.
"Every time I opened my mouth about that case, I said maybe two or three main points and one of them is 'violence knows no country, no religion, no boundaries'," Holton said.
He added that not referring to him as a Muslim made him the target of Islamophobic bloggers.
"Of all the hateful things that have been said about me as U.S. Attorney, it's part of the job, right, having to deal with the bloggers comments -- and believe me the medical marijuana crowd does not love me -- but of all the hateful things that have been said about me was in response to me saying that," Holton said. "There are people who don't get it."
Holton called the outreach he did with the Muslim community over the course of his tour as U.S. Attorney for Oregon the most important work of his career, joking that he put on "10 pounds in lamb weight" and recalling having 15 to 20 imams over at his house for a halal meal that went until 2 a.m.
"My wife jokes that our social life has been taken over by Muslim engagement," said Holton.