After an hourlong meeting with Muslim community leaders, Bush said last week's murderous acts by Islamic terrorists "violate the fundamental tenets of the Islamic faith."
In keeping with custom, Bush removed his shoes before entering the mosque.
Bush's remarks came in the aftermath of several weekend killings that are being investigated as possible hate crimes against those of Middle Eastern origin, as well as hundreds of reports of anti-Muslim and anti-Arab harassment and discrimination.
"Islam is peace," Bush said at the center, which is near the vice president's residence and in the heart of the embassy district. "These terrorists don't represent peace. They represent evil and war."
Speaking to reporters, Bush said Americans who are intimidating fellow citizens represent the "worst of humankind."
He said the Muslim leaders with whom he met share his outrage and sadness. "They love America just as much as I do."
Bush's remarks from the main prayer room of the mosque were broadcast live to the entire Arab-speaking world, from Morocco to the Iranian border, said a spokesman for Voice of America.
Outside the Islamic Center, where Washington's Muslims come to pray up to five times a day, many said they were feeling insecure in the wake of the attack on the nation and grateful the president had come to deliver a message of support.
"We all feel terrible about what has happened - and bad about what's happening now to us," said Tariq Syed, a law student whose family is from India. "The politicians are doing a good job of explaining that the terrorism was the act of a few people and does not represent our religion."
Syed said he's noticed suspicious glances, directed especially at Muslim women who wear scarves to cover their head, and heard mutterings. For his part, he decided against wearing an Arabic outfit to a wedding he attended in a small town in Pennsylvania over the weekend in favor of a suit.
"I thought it might be in my interest," he said.
Since last week's attack, the FBI has opened 40 hate crime inquiries nationally. FBI Director Robert S. Mueller said yesterday that agents were investigating two killings, as well as assaults, arsons and threats that may have been ethnically motivated.
Mueller would not disclose details, but James Zogby, president of the Arab-American Institute said he knew of three murders that had taken place over the weekend that are suspected of being hate crimes: the killing of a Sikh gas station owner in Mesa, Ariz., a Pakistani grocer in Dallas and an Egyptian in San Gabriel, Calif.
Many of the suspected retaliatory hate crimes have been directed at Muslim centers of worship and Muslim community centers, said Mueller, warning that civil rights violations would be vigorously investigated.
"I'll make it very clear - vigilante attacks and threats against Arab-Americans will not be tolerated," he said.
The Council on American-Islamic Relations said it had received several hundred reports of anti-Muslim harassment, threats, discrimination and violence in the past week and called on law enforcement agencies to step up protection of Muslim institutions and businesses.
The council accused the FBI and local law enforcement officials of questioning people of Middle Eastern origin based on appearance or name.
The practice of "racial profiling" was the subject of volatile debate in this country before last week. Nihad Awad, executive director of the council, said he fears that innocent people who had nothing to do with last week's attacks are being intimidated and harassed.
Mueller sharply denied that, saying individuals who have been questioned were singled out because agents believed they had information relevant to the probe. "We do not, have not, will not target people based solely on their ethnicity - period, point-blank."
Zogby said he had fully expected a violent backlash, because such anti-Arab sentiments had followed the Oklahoma City bombing and the crash of TWA Flight 800 - even though neither disaster involved Arabs.
But he said the effort by the nation's leaders has dulled some of the misdirected anger. He pointed to unanimous House approval Saturday condemning acts of "bigotry and violence" against Arab-Americans, Muslims and South Asians living in this country. "Something new is happening," he said. "Public support is competing with the backlash. It didn't used to."
Zogby said 90 percent of the e-mail he has received has been supportive. And his polling is showing that 62 percent of Americans have a favorable attitude toward Arab-Americans. Only 8 percent of respondents said they consider the United States to be at war with Islam as a whole.
Islam is one of the fastest growing religions in this country and around the world. There are an estimated 7 million Muslims in America, and 1.2 billion worldwide.
Some in Washington said their sadness at the terrorist attack was compounded by their concern about perceptions of their religion and heritage.
"I can deal with people stigmatizing me," said Amar Sall, a Senegalese educator who lives in Silver Spring. "What I cannot deal with is people thinking Islam may have anything to do with what's happened. That is mind-blowing."
Sall said he worries about the safety of his four school-age children, but that they've not been subjected to harassment. "You see people looking at you, thinking, 'He's one of them.' It hurts."
Ahmad Jaser, a Jordanian carpenter who lives in Rockville, had recently been hired for an eight-month project to help build a new house when, the day after the terrorist attack, he and a worker from Senegal were abruptly fired.
Told by the foreman that the contractor had decided to bring in his own crew, Jaser said he didn't know whether his firing had anything to do with his background, but suspected it might.
"They were asking where we were from," said Jaser, 45, who has lived in the United States for 23 years. "The next day, we go there, no more job."
Many Muslims said relatives in their homelands had besieged them with worried phone calls.
Nafissatou Diouf, a receptionist at the Islamic Center, said her parents have been calling from Senegal, urging her to stop wearing her hijab, or scarf. She has stopped wearing it outside the mosque, she says, for fear that someone who lost a loved one in the attacks might take out their anger on her.
"I'm still proud to be a Muslim," she said. "But we understand."
Sun staff writer Gail Gibson contributed to this article.