An Army spokesman says "a relatively small number of Muslims" at the Pentagon felt the invitation was inappropriate because of Rev. Franklin Graham's past anti-Islamic comments.
But Lieutenant Colonel Ryan Yantis says Christians at the Pentagon had asked for Graham, and the Pentagon tries to accommodate the worship needs of all religious groups.
Yantis notes that separate Muslim services are scheduled at the Pentagon the same day because Friday is the Islamic sabbath.
Graham was heavily criticized for calling Islam "a very evil and wicked religion" in an interview with NBC not long after the terrorist attacks on New York and Washington.
He wrote in a subsequent Wall Street Journal column that he does not believe Muslims "are evil people because of their faith. But I decry the evil that has been done in the name of Islam, or any other faith - including Christianity."
"I believe it is my responsibility to speak out against the terrible deeds that are committed as a result of Islamic teaching," he wrote, singling out the repressive treatment of women, and the absence of religious expression, in some Muslim countries.
He also said that "the persecution or elimination of non-Muslims has been a cornerstone of Islam conquests and rule for centuries," and has since made other comments attacking Muslim for lack of religious tolerance.
Graham, son of famed evangelist Billy Graham, recently sparked fresh anger with plans to send Christian relief workers into Iraq when the war ends.
Samaritan's Purse, the relief agency headed by Graham, is poised to provide shelter, water and medical assistance inside Iraq as soon as military clearance is available.
"As American and allied troops roll into Iraq, Samaritans Purse has a well-equipped team already on the ground in the Middle East ready to help thousands of suffering families in the name of Jesus Christ," a statement on the group's Web site says.
Workers can provide drinking water for up to 20,000 people, materials to build temporary shelters for more than 4,000 families, and household items and medical kits to meet the needs of up to 100,000 people for three months, Graham has said.
But some Muslim groups believe Graham has ulterior motives.
"Given his past viewpoints, people are suspicious about his real aim, which could be to take advantage of a situation in which people are desperate," said Hodan Hassan, a spokeswoman for the Council on American-Islamic Relations in Washington, D.C. "They will have food in one hand and the Bible in the other."
Graham's group is one of several Christian relief agencies planning to provide war aid. Most do not proselytize, and believe just helping others sends a message about Christian faith.
But a spokesman for Graham's group has said religious issues might be raised.
"We do not deny the name of Christ," Ken Isaacs of Samaritan's Purse told Newhouse News Service. "We believe in sharing him in deed and in word. We'll be who we are."
Graham's comments were in stark contrast to efforts by President Bush to separate his avowed respect for Islam from any U.S. anti-terrorist action.
After initially referring to the war on terrorism as a "crusade" and calling it Operation Infinite Justice — lingo that offended some Muslims — the president has said repeatedly that Islam is "a great religion," and has accused terrorists of profaning it.
However, the White House angered Muslim groups last week when it nominated commentator Daniel Pipes to the board of the U.S. institute of Peace. Pipes said the grenade attack on U.S. troops in Kuwait by a Muslim-American serviceman demonstrates "the suspect allegiance of some Muslims in government."
He earlier wrote that, "There is no escaping the unfortunate fact that Muslim government employees in law enforcement, the military and the diplomatic corps need to be watched for connections to terrorism."
Asked about the Graham invitation, Pentagon spokesperson Victoria Clarke said the chaplain's office "invites speakers and religious leaders from all sorts of different places representing all sorts of different faiths and organizations."
She said of actions in Kosovo, Somalia, Afghanistan and Iraq, "Clearly were doing this for the benefit of the Muslim people."