Washington (CNN) President Barack Obama, speaking at his summit on countering violent extremism Wednesday, sought to strike a balance between appealing for more acceptance of Muslim-Americans while emphasizing the need to remain vigilant against radicals who could turn violent.

"We are not at war with Islam. We are at war with people who have perverted Islam," Obama said during his remarks, adding later that Muslim leaders "need to do more to discredit the notion that our nations are determined to suppress Islam."

Obama went to lengths before the summit began to avoid linking extremism to the Muslim faith; his intent, aides say, was to avoid giving credence to the ideologies of Islamic State or al Qaeda terrorists.

On Wednesday he sought to explain his wording, declaring al Qaeda and ISIS "desperate for legitimacy."

"They try to portray themselves as religious leaders, holy warriors in defense of Islam," he said. "We must never accept the premise that they put forward because it is a lie. Nor should we grant these terrorists the religious legitimacy that they seek. They are not religious leaders. They are terrorists."

Obama called for resilience in the face of terrorist threats and pointed to efforts in U.S. cities where Muslim communities and law enforcement are making strides in addressing the root causes of violent extremism.

"We all know there is no one profile of a violent extremist or terrorist. There is no way to predict who will become radicalized," he said. "We are here at this summit because of the urgent threat from groups like al Qaeda and ISIL and this week, we are focused on prevention."

During Wednesday's session, the White House highlighted pilot programs in three metropolitan areas -- Boston, Los Angeles, and the Twin Cities -- where law enforcement and Muslim-American groups are trying to join forces to counter violent extremism.

Officials say they hope to replicate those programs in other places around the country with populations that could be prone to radicalization.

"This is really a moment to rededicate ourselves to efforts that really reach out to communities, and build that confidence that they need to have so that they feel comfortable working with authorities, both to prevent radicalization and also, when necessary, to intervene," said one senior administration official.

That strategy has drawn criticism from civil rights organizations, who say the government risks alienating Muslim communities by partnering with religious and cultural organizations to identify potential extremists.

"From conceptualization to implementation, the CVE strategy raises significant constitutional and privacy concerns. It is not based on empirical evidence of effectiveness. It threatens to do more harm than good," said Hina Shamsi, the director of the American Civil Liberties Union National Security Project.

Officials attending the White House summit downplayed those fears, arguing the pilot programs established across the country were providing needed outreach to communities, and weren't spying on them.

"This has nothing to do with intelligence, it has nothing to do with surveillance, this is about developing healthier, resilient communities," said Michael Downing, the Deputy Chief and commanding officer of the Los Angeles Police Department's counterterrorism and special operations bureau.

He also pointed to the case in Chapel Hill, North Carolina, where Muslim Americans were the victims in a high profile murder case. The outcry from Muslim American groups led to a mass prayer outside the White House last week.

"We do not yet know why three young people, who were Muslim Americans, were brutally killed in Chapel Hill, N.C. But we know that many Muslim Americans across our country are worried and afraid," Obama wrote in the op-ed.