Wading deeper into the debate over violence inspired by radical Islam, President Obama Thursday equated terrorism with “terrible deeds” committed by Christians in centuries past, comments that quickly sparked disgust among conservatives.

Speaking at the National Prayer Breakfast in Washington, Mr. Obama said Christians can’t lay claim to a higher moral ground in discussions of how to confront violent extremist groups such as the Islamic State, also known as ISIS or ISIL.

“Unless we get on our high horse and think this is unique to some other place, remember, during the Crusades and the Inquisition, people committed terrible deeds in the name of Christ,” Mr. Obama said. “In our home country, slavery and Jim Crow all too often [were] justified in the name of Christ. It is not unique to one group or one religion. There is a tendency in us, a sinful tendency, that can pervert and distort our faith.”

His comments, in the wake of the president’s much-publicized reluctance to utter the phrase “radical Islam” out of concern that he’ll alienate moderate Muslims, drew angry reactions from some Christians and accusations that Mr. Obama was inadvertently offering justification for Islamist extremists.

Former Virginia Gov. Jim Gilmore said the president’s comments “are the most offensive I’ve ever heard a president make in my lifetime.”

“He has offended every believing Christian in the United States,” said Mr. Gilmore, a Republican. “This goes further to the point that Mr. Obama does not believe in America or the values we all share. There is no moral equivalency for the horrific behavior of terrorists whose atrocities are shocking and reprehensible.”

Catholic League President Bill Donohue said Mr. Obama should apologize for “an attempt to deflect guilt from Muslim madmen.” He said the president’s comparisons of modern-day terrorism to the Crusades and the Inquisition were “insulting” to Christians.

“Obama’s ignorance is astounding, and his comparison is pernicious,” Mr. Donohue said. “The Crusades were a defensive Christian reaction against Muslim madmen of the Middle Ages.”

Steven Bucci, director of foreign and national security policy at the conservative Heritage Foundation, said the president’s comparisons were “absurd.”

“The president has a tendency to mix philosophical or religious thought with his political agenda,” Mr. Bucci said. “I just wish he would take the time to understand how it’s going to be perceived and the unintended consequences of the messages he sends. In this case, it’s not just to mollify the moderate Muslim world, but it’s frankly going to be seen as succor to radical Islam. I think he was off-mark.”

At the prayer breakfast, Mr. Obama condemned all acts of violence in the name of religion, referring to the Islamic State as a “death cult.”

“No God condones terror,” he said. “As people of faith, we are summoned to push back against those who try to distort our religion — any religion — for their own nihilistic ends.”

But the president also suggested he disagreed with the satirical French newspaper that provoked deadly terrorist attacks last month by poking fun at Islam. He said people of faith are obligated “to condemn such insults,” and his comments offered a possible explanation for why he failed to attend the unity march in Paris with other world leaders in support of free speech after the attacks.

“If in fact we defend the legal right of a person to insult another’s religion, we’re equally obligated to use our free speech to condemn such insults and stand shoulder to shoulder with religious communities, particularly religious minorities who are targets of such attacks,” Mr. Obama said. “Just because you have the right to say something doesn’t mean the rest of us shouldn’t question those who would insult others in the name of free speech.”

Mr. Obama never directly mentioned the newspaper, Charlie Hebdo, that was the scene of a terrorist attack in Paris that left 12 dead. The Islamist militants who carried out the attack said they were seeking revenge for the newspaper’s caricatures of the Prophet Muhammad that offended many Muslims.

Referring to the global fight against terrorism, Mr. Obama criticized those who pervert Islam to carry out violent attacks.

“From a school in Pakistan to the streets of Paris, we have seen violence and terror perpetrated by those who profess to stand up for their faith — profess to stand up for Islam but in fact are betraying it,” Mr. Obama said. “We see [the Islamic State], a brutal, vicious death cult that, in the name of religion, carries out unspeakable acts of barbarism, terrorizing religious minorities.”

Mr. Bucci said the president appropriately criticized terrorists for twisting Islam for their violent aims, but said he should have stopped there.

“To draw moral equivalents to that — what’s the point of that?” Mr. Bucci asked. “Is he trying to make ISIS feel better about themselves? He doesn’t want to hurt their self-image? I find the pretzellike twisting of his logic to be so overwrought as to be absurd. I mean, ISIS isn’t going to this much trouble to justify itself.”

Some observers questioned the historical accuracy of Mr. Obama’s assertions. Mr. Donohue, for example, said the Crusades were a response to Muslim invasions and brutal occupation of the Holy Land. And he said the Catholic Church had “almost nothing to do with” the Inquisition, which he said was largely carried out by secular authorities.

Mr. Obama also said the freedom of religion in the U.S. protects those who don’t believe in God.

“We will constantly reaffirm that fundamental freedom, freedom of religion, the right to practice our faith how we choose, to change our faith if we choose, to practice no faith at all if we choose and to do so free of persecution and fear and discrimination,” he said.

The prayer breakfast has become something of a minefield for Mr. Obama. At the same event in 2013, keynote speaker Ben Carson, a conservative neurosurgeon, gave the president a face-to-face comeuppance with comments that criticized the course of the country and Obamacare.

Organizers of the breakfast told Mr. Carson that he should apologize to the president, a suggestion he declined. Mr. Carson is a likely candidate for the Republican nomination for president in 2016.

This year’s keynote speaker, NASCAR great Darrell Waltrip, evoked laughter when he made a reference to Mr. Carson.

“I’m not a brain surgeon, and I’m not running for office,” Mr. Waltrip said. “So I’m the perfect guy to be here this morning.”

Then he turned to the president and said, “I hope that was OK. My wife told me I maybe shouldn’t say that.”

Among those in the audience at the Washington Hilton was the Dalai Lama, whom the president called out for praise.

“He inspires us to speak up for the dignity and freedom of all human beings,” Mr. Obama said.

The Council on American-Islamic Relations, the nation’s largest Muslim civil rights and advocacy group, praised Mr. Obama’s remarks.

“We thank President Obama for clearly separating the brutal actions of ISIS from the faith of Islam and for reminding us all that violence and injustice are not part of any faith,” said CAIR National Executive Director Nihad Awad. “We invite the president to show public support for American Muslims by making the symbolic but significant gesture of visiting an American mosque in this time of growing Islamophobia.”

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