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Is the FBI doing its best to combat terrorism?

In an exclusive interview with NBC News, the FBI's highest-ranking Arab-American agent speaks out, saying a lack of expertise and critical skills are hurting America's ability to deal with terrorist threats.

Bassem Youssef is the FBI's highest-ranking Arab-American agent. He's fluent in Arabic, ran the FBI's offices in Saudi Arabia and is a terrorism expert. In fact, Youssef's undercover work helping to infiltrate the terror organization of the so-called "blind sheik," Sheik Omar Abdul Rahman, earned him the intelligence community's most-prestigious award, the National Intelligence Distinguished Service Medal.

But now, for the first time, Youssef is speaking out against the agency he loves.

"I don't believe that the FBI's doing everything it can to combat terrorism," the 18-year FBI veteran tells NBC News.

Though he's one of only six FBI agents with advanced Arabic skills, Youssef believes that, since 9/11, the FBI has blocked him from playing a significant role in the war on terror. He claims discrimination, and sued the FBI in 2003.

"To be totally set aside, blackballed since 9/11, makes absolutely no sense," he says.

Beyond Youssef's own employment claims, depositions of nearly a dozen top FBI officials in his case have exposed what critics say are serious shortcomings in the FBI's approach to counterterrorism. The taped depositions, which have never been aired before, seem to reveal a stunning lack of knowledge about some terrorism basics.

Terrorism 101
Dale Watson, now retired, was the FBI's top counterterrorism official before and after 9/11.

In a deposition taken on Dec. 8, 2004, Youssef’s lawyer Stephen Kohn asked Watson: “Do you know who Osama bin Laden's spiritual leader was?"

Watson: Can't recall.

Lawyer: And do you know the differences in the religion between Shiite and Sunni Muslims?

Watson: Not technically, no.

John Lewis was until recently the FBI’s deputy assistant director of counterterrorism. During his deposition on May 17, 2005, he was asked if he knew the difference between Shiites and Sunnis.

Lewis: You know, generally. Not very well.

Lawyer: Was there any relationship between the first World Trade Center bombing and the 9/11 attacks?

Lewis: I'm aware of no immediate relationship other than all emanates out of the Middle East, al-Qaida linkage, I believe. Not something I've studied recently that I'm conversant with.

Counterterrorism experts say such apparent ignorance of the enemy is alarming.

“Not knowing these basic tenets is symptomatic of a lack of deep knowledge about your principal adversary, and that is unacceptable," says Michael Sheehan, an NBC News terrorism analyst.

Senior FBI officials argue on the tapes that it's not necessary to have expertise in Arab culture — even in terrorism — to run the FBI's war on terror. It's leadership that matters most, they say.

"The subject-matter expertise is helpful, but it is not a prerequisite. That's not what I look for," said Gary Bald, the former executive assistant director for the National Security Branch of the FBI, in his March 14, 2005, deposition.

However, Youssef says expertise is critical in evaluating threats, recruiting informants and allocating resources.

NBC News: You're saying the biggest problem is the FBI still doesn't have the expertise to effectively fight the war on terror?

Youssef: Yes, I believe that is the case. If you can't get inside the mind of the enemy, we will never succeed.

Five years after 9/11, critics say the FBI has been slow to hire agents with Arabic skills or knowledge. In fact, only 33 of the FBI’s 12,000 agents have even a limited proficiency in Arabic, the agency says. Until recently, new agents used to get just two hours of Arabic culture training at the FBI facility in Quantico, Va. They now receive 12 hours of instruction in Islam and the evolution of militant Islamic ideology, plus much more extensive counterterrorism training.

FBI spokesman John Miller concedes that subject-matter expertise does matter in counterterrorism.

"To have that depth of subject-matter expertise and the executive and leadership skills is certainly a plus," Miller says.

Miller adds that while top FBI officials may not have been able to pass a lawyer’s pop quiz version of Jihad Jeopardy, the FBI has brought in and trained a new generation of agents and supervisors with years of frontline experience handling terror cases.

"To ask them to go back and pick out details from cases from years ago, or other questions that I refer to as kind of Trivial Pursuit, they have analysts working for them who have those answers cold," Miller says. "That is not necessarily their function at the top."

Miller adds that the FBI is working hard to increase its pool of six fluent, Arabic-speaking agents.

"It's not enough. And it's not for lack of trying," he says. "But you can't just focus on agents.  We've tried to break down the walls between agents, analysts and language analysts.  They now work as a team, and we have doubled the number of language analysts and increased by 300 percent the number of Arab speakers among them.  We still need to build on those numbers, but we have vastly improved."

Justice Department watchdog
A Justice Department watchdog recently ruled that the FBI had blocked Youssef from getting a counterterrorism job because, in part, Youssef had angered and embarrassed FBI Director Robert Mueller at a face-to-face meeting with a prominent U.S. congressman. The DOJ’s Office of Professional Responsibility wrote in July that Mueller and senior FBI officials were upset when Youssef complained to Rep. Frank Wolf, R-Va., that Youssef’s counterterrorism training and Arabic skills weren't being used after 9/11.

The FBI says in legal filings that it never discriminated against Youssef. Miller says he can’t discuss the merits of the case because it is still in litigation. However, some FBI agents privately grumble that Youssef has an inflated sense of his own worth, and used poor judgment in taking on the FBI at the meeting with Mueller and Wolf.

Youssef says he never meant to be disloyal or to air his problems outside the family.

"I had gone through every possible channel that I could think of within the family, and nothing was done," he says.

Youssef says he will not give up his fight.

"I think every American would do whatever they can to fight terrorism, because we will never forget 9/11," he says. "And having worked counterterrorism for so many years and not to do it, that devastates me."

For now, Youssef has a desk job with the FBI running a squad that analyzes links between telephone calls — a far cry from terrorism's frontlines.