Before the Boston Marathon bombings, the Obama administration argued for years that there is a big difference between terrorists and the tenets of Islam.

A senior White House aide in 2009 publicly urged Washington to cease using the term “jihadist” — asserting that terrorists are simply extremists. Two years later, the White House ordered a cleansing of training materials that Islamic groups deemed offensive.

Now, some analysts are asking whether the 2009 edict and others that followed have dampened law enforcement’s appetite to thoroughly investigate terrorism suspects for fear of offending higher-ups or the American Muslim lobby.

It is not just the case of Tamerlan Tsarnaev, a radicalized jihadist whom the FBI questioned in 2011 and cleared of terrorism links. At least five Muslims have attempted mass destruction in the U.S. since 2009, undetected beforehand by law enforcement and the intelligence community:

• Abdulhakim Mujahid Muhammad opened fire at a military recruiting office in Little Rock, Ark., in June 2009, killing one soldier.

• Najibullah Zazi, who said he was a member of al Qaeda, tried to detonate bombs in New York City’s subway in September 2009.

• Army Maj. Nadal Malik Hassan opened fire at a soldier processing center at Fort Hood, Texas, killing 13.

• Umar Farouk Abdulmutallab tried to explode a bomb hidden in his underwear onboard a flight to Detroit in December 2009.

• Faisal Shahzad attempted to detonate a car bomb in Times Square in May 2010.

Steven Emerson runs the Investigative Project on Terrorism, which monitors a network of Islamic groups with ties to the Muslim Brotherhood, whose stated goal is to impose Shariah, or Islamic law, on the world.

“Numerous experts on Islamic terrorism like myself and I had given 143 lectures at the FBI, CIA were banned from speaking to any U.S. government counterterrorism conferences,” Mr. Emerson told The Washington Times. “Instead, these agencies were ordered to invite Muslim Brotherhood front groups.”

The biggest White House push to tone down training on jihadists emerged in 2011, the same year the Russian government warned the U.S. about Tamerlan Tsarnaev, whose parents hailed from Chechnya, a hotbed of radical Islamists. Tamerlan and younger brother Dzhokhar Tsarnaev are accused of placing the two bombs that killed three and wounded more than 260 at the Boston Marathon.

Islamic backlash

In October 2011, 57 Islamic groups wrote a letter to John O. Brennan, now CIA director, but then President Obama’s chief counterterrorism adviser.

Citing news reports, the groups complained of “biased, false and highly offensive training materials about Muslims and Islam” inside the federal government’s instructional halls.

“While recent news reports have highlighted the FBI’s use of biased experts and training materials, we have learned that this problem extends far beyond the FBI and has infected other government agencies, including the U.S. Attorney’s Anti-Terrorism Advisory Councils, the U.S. Department of Homeland Security, and the U.S. Army,” the letter read.

Muslims objected to several training guides, such as a 2009 report produced at the Army Command and General Staff at the Fort Leavenworth School of Advanced Military Studies.

“Moderate Muslims are not exercising moderation; they are simply applying other means to accomplish the same goal of establishing global Islamic dominance,” it quoted the report as saying.

At least two of the 57 groups were listed by the Justice Department as unindicted co-conspirators and as being connected to the Muslim Brotherhood in the prosecution of a Texas charity for funding Hamas, a U.S.-designated terrorist organization. The groups are the Council on American Islamic Relations (CAIR) and the Islamic Society of North America.

The organizations’ letter demanded that biased trainers be disciplined, that all instructors undergo retraining and that materials deemed offensive by Muslim activists be purged.

The White House issued an edict to scrub all law enforcement, intelligence and military teachings on Islam. The FBI ended up discarding pages of information that warned about the threat from the Brotherhood.

John Guandolo, a former FBI counterterrorism agent, has spent years studying the global Muslim Brotherhood movement and its links to American Islamic groups. The FBI relies on some of them to guide its training. The political left has branded Mr. Guandolo an “Islamophobe.”

“There is no strategy in the FBI,” he told The Times. “At FBI headquarters, it is a daily fire drill. The threats come in, and they run around to deal with them and run them down. But because none of it can have anything to do with the Muslim Brotherhood’s movement in the U.S. or Islam, they never address the root cause and common investigative realities.”

Mr. Emerson, who maintains back-channel ties to law enforcement, said any slide presentation on Islamic extremism now has to be submitted to a special Justice Department panel.

He said one slide that was required to be omitted showed the famous photo of captured Sept. 11 mastermind Khalid Shaikh Mohammed. The photo of a disheveled and unshaven Mohammed was deemed “offensive to Islam,” Mr. Emerson said.

Political correctness

Perhaps the best-known casualty of the White House order is Army Lt. Col. Matthew Dooley, a decorated officer who taught at the Joint Forces Staff College in Norfolk, Va. After learning of Col. Dooley’s course and its “outside the box” scenario of nuclear war, Army Gen. Martin E. Dempsey, the Joint Chiefs chairman, launched investigations that ended with the officer’s firing.

A briefing by Col. Dooley, whose course “Perspectives on Islam and Islamic Radicals” had been approved by his supervisors, discussed how “political correctness” prevents the military from talking about radical Islam.

“Political Correctness is killing us: How can we properly identify the enemy, analyze his weaknesses, and defeat him, if we are NEVER permitted to examine him from the most basic doctrinal level?” the briefing read.

Early in Mr. Obama’s first term, Mr. Brennan set the tone for a softer line on Islam and its links to terrorism.

In August 2009, he went to the Center for Strategic and International Studies in Washington to talk on the theme “A New Approach to Safeguarding Americans.”

He said the president does not “see this challenge as a fight against ‘jihadists.’ Describing terrorists in this way — using a legitimate term, jihad, meaning to purify oneself or to wage a holy struggle for a moral goal — risks giving these murderers the religious legitimacy they desperately seek but in no way deserve.”

Some analysts disagree with that interpretation, saying the Koran clearly states that jihad is a “holy war.”

Mr. Brennan and other aides preferred the title “violent extremists” over Islamic terrorists.

In 2011, Sen. Joe Lieberman, Connecticut independent, was among those in Congress who disliked the fuzzy term.

“They say our enemy is violent extremism,” Mr. Lieberman said. “It’s not. It’s not animal rights extremists or white supremacy extremists. It’s Islamic extremism.”

Sen. Marco Rubio, Florida Republican, told Fox News this week that the administration will not recognize the terrorists for what they are — radicalized Islamists.

“My problem with this administration is they refuse to acknowledge the existence of this kind of terrorism,” Mr. Rubio said.

He noted that after the Sept. 11 terrorist attack on the U.S. diplomatic complex in Benghazi, Libya, the White House refused to call it terrorism and blamed it on everyday demonstrators.

“And even now, irrespective of whether [the Tsarnaev brothers] met with extremists or not when they went to Russia, the bottom line is they were radicalized and they carried out an attack because of that ideology,” Mr. Rubio said. “This is the emerging face of terrorism against the United States by radical Islamists, and we have to have security systems that recognize that and can deal with that because the No. 1 job of the federal government is to secure our national security.”

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