Daryl Johnson had a sinking feeling when he started seeing TV reports on Sunday about a shooting in a Wisconsin temple. "I told my wife, 'This is likely a hate crime perpetrated by a white supremacist who may have had military experience,'" Johnson recalls.

It was anything but a lucky guess on Johnson's part. He spent 15 years studying domestic terrorist groups -- particularly white supremacists and neo-Nazis -- as a government counterterrorism analyst, the last six of them at the Department of Homeland Security. There, he even homebrewed his own database on far-right extremist groups on an Oracle platform, allowing his analysts to compile and sift reporting in the media and other law-enforcement agencies on radical and potentially violent groups.

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But Johnson's career took an unexpected turn in 2009, when an analysis he wrote on the rise of "Right-Wing Extremism" (.pdf) sparked a political controversy. Under pressure from conservatives, the Department of Homeland Security (DHS) repudiated Johnson's paper -- an especially bitter pill for him to swallow now that Wade Michael Page, a suspected white supremacist, killed at least six people at a Sikh temple in Oak Creek, Wisconsin. For Johnson, the shooting was a reminder that the government's counterterrorism efforts are almost exclusively focused on al-Qaida, even as non-Islamist groups threaten Americans domestically.

"DHS is scoffing at the mission of doing domestic counterterrorism, as is Congress," Johnson tells Danger Room. "There've been no hearings about the rising white supremacist threat, but there's been a long list of attacks over the last few years. But they still hold hearings about Muslim extremism. It's out of balance." But even if that balance was reset, he concedes, that doesn't necessarily mean the feds could have found Page before Sunday's rampage.

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Johnson left DHS in April 2010 after "they dissolved my team," he says. Had he still been at DHS, he says he would have published an analysis calling attention to a growing number of attacks on mosques, which he thinks could serve as a "warning" to Sikh communities that are often mistaken for Muslim ones. But finding so-called "lone wolf" terrorists like Page is a challenge no matter their motivations, since they operate outside established extremist cells and often don't have criminal records, making it difficult for law enforcement or homeland security officials to spot them.

Now a security consultant in the Washington D.C. area, Johnson used to work for DHS' analysis shop, the Office of Intelligence and Analysis (I&A). He supervised a team of six analysts studying what he calls "domestic non-Islamic extremism." It's a telling term: the DHS employed as many as 40 analysts who looked at al-Qaida and other jihadist groups' inroads into the homeland.

Johnson ran everything else. One person on his team worked on the threat from anarchists; another, the threat from animal-rights extremists. Still others looked at anti-abortion radicalism, white supremacy and radical environmentalism. They were supplemented by analysts at the FBI and the Bureau of Alcohol, Tobacco and Firearms; but outnumbered by the literally thousands of analysts, operatives and other counterterrorism officials throughout the government who focus on jihadism. "Salaries were our major budget item," he recalls.

Then, in April 2009, Johnson warned that the election of the first African-American president, combined with recession-era economic anxieties, could fuel a rise in far-right violence. "DHS/I&A is concerned that rightwing extremists will attempt to recruit and radicalize returning veterans in order to boost their violent capabilities," he wrote.

And so began a brief media firestorm. Conservative writers feared that the DHS was demonizing -- even, potentially, criminalizing -- mainstream right-wing speech. "It's no small coincidence that [Secretary Janet] Napolitano's agency disseminated the assessment just a week before the nationwide April 15 Tax Day Tea Party protests," pundit Michelle Malkin speculated in the Washington Times. Others objected that Johnson's report unfairly stigmatized veterans.

It surprised Johnson. An Eagle Scout leader from northern Virginia in his early 40s, Johnson became interested in counterterrorism in his teens, after an Arkansas standoff between federal authorities and a millenarian group called The Covenant The Sword And The Arm of The Lord, which stockpiled weapons and explosives to bring about Armageddon. "I was always fascinated with why people use religion to justify violence and believe the world was ending -- and had a role to play in hastening that end," Johnson said.

Stung, DHS responded by cutting "the number of personnel studying domestic terrorism unrelated to Islam, canceled numerous state and local law enforcement briefings, and held up dissemination of nearly a dozen reports on extremist groups," the Washington Post reported in June 2009.

According to Johnson, his former team now consists of a single analyst tasked with tracking all domestic non-Islamic extremism. His database has been shuttered.

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Asked for comment, DHS disputed Johnson's claim that it gives non-Islamic extremism short shrift.

"The Department of Homeland Security protects our country from all threats, whether foreign or homegrown, and regardless of the ideology that motivates its violence," spokesman Matt Chandler told Danger Room. "we face a threat environment where violent extremism is neither constrained by international borders, nor limited to any single ideology. This is not a phenomenon restricted solely to any one particular community and our efforts to counter violent extremism (CVE) are applicable to all ideologically motivated violence. DHS continues to work with its state, local, tribal, territorial and private partners to prevent and protect against potential threats to the United States by focusing on preventing violence that is motivated by extreme ideological beliefs."

Johnson, who has written a forthcoming book about far-right extremist groups, concedes that the definition of "right-wing" in his product was imprecise. In retrospect, he says he should have clarified that his focus was on "violent" right-wing organizations, like white supremacists, neo-Nazis and so-called Sovereign Citizens who believe the U.S. government is an illegitimate, tyrannical enterprise. Much like mainstream Muslims denounce terrorism and object to over-broad analysis portraying Islam as an incubator of extremism, so too do mainstream conservatives denounce neo-Nazis and white supremacists and dispute that those groups are authentically right-wing.

Nor does he think DHS should ignore Islamic extremism. "It just needs to be more balanced," Johnson says. New York congressman "Peter King has held three hearings in the past year on Muslim extremism," he says, referring to the chairman of the House Homeland Security Committee, "but he's yet to have a single hearing on right-wing extremism when there's been a lot more activity."

Indeed, since Johnson released his ill-fated report, the Wichita, Kansas, abortion doctor George Tiller was assassinated; a security guard was killed when a gunman with neo-Nazi ties went on a shooting spree at the U.S. Holocaust Museum; the FBI arrested members of a Florida neo-Nazi outfit tied to drug dealing and motorcycle gangs; a man was charged with attempting to detonate a weapon of mass destruction at a Spokane, Washington march commemorating Martin Luther King Jr.'s birthday; and several mosques around the country have been vandalized or attacked -- including a Missouri mosque that burned to the ground on Monday, which had been attacked before.

As Salon recounts, the FBI has been warning for years that far-right racialist organizations might be interested in suicide terrorism. Peter Bergen, a longtime chronicler of al-Qaida, wrote on Tuesday that far-right domestic terrorism rivals and might eclipse the threat of homegrown jihadism.

In a press conference on Monday, FBI Special Agent-in-Charge Teresa Carlson acknowledged that Page, the perpetrator of the Sikh temple assault, "had contact with law enforcement in the past," but that contact didn't rise to the level of sparking an active investigation. The Southern Poverty Law Center, which tracks right-wing extremist groups, has apparently had Page on its radar for some time.

But Johnson doesn't contend that more resources would necessarily have stopped Page from attacking the Sikh temple. Lone-wolf terrorists are hard to spot. What the government should do instead is broaden its counterterrorism focus beyond just jihadis. "It needs to be more balanced," Johnson says. "It's frustrating to see these types of incidents ongoing."