In a statement, Army Lt. Gen. William G. Boykin said he never meant to offend Muslims.
"I am not anti-Islam or any other religion," Boykin said. "I support the free exercise of all religions. For those who have been offended by my statements, I offer a sincere apology."
Pentagon officials released Boykin's statement late Friday after spending hours deliberating how to calm the storm of criticism surrounding Boykin's comments. The general's statements came in speeches - some made in uniform - at evangelical Christian churches.
In several speeches, Boykin said the real enemy was not Osama bin Laden but Satan.
"I have frequently stated that I do not see this current conflict as a war between Islam and Christianity," Boykin said. "I have asked American Christian audiences to realize that even though they cannot be in Iraq or Afghanistan, they can be part of this war by praying for America and its leaders."
A decorated veteran of foreign campaigns, the three-star general said of a 1993 battle with a Muslim militia leader in Somalia: "I knew that my God was bigger than his. I knew that my God was a real God, and his was an idol." After the man was captured, Boykin said he told the man, "You underestimated our God."
Boykin's statement said that comment was misinterpreted.
"My comments to Osman Otto in Mogadishu were not referencing his worship of Allah but his worship of money and power; idolatry," Boykin said. "He was a corrupt man, not a follower of Islam."
Critics have said Boykin's remarks could undermine a more than two-year Bush administration effort to promote good relations with Muslims in America, as well as play into the hands of those who have fanned anti-Americanism abroad by casting the counter-terror war as an attack on Islam.
Asked about the general's church comments, Adel al-Jubeir, the foreign affairs adviser to Saudi Crown Prince Abdullah, told reporters Friday: "If true, outrageous. I thought they were insensitive. I thought they were unbecoming of a senior military official, and certainly unbecoming of a senior government official."
Boykin, the deputy undersecretary of defense for intelligence, has told Pentagon officials that he will curtail his speechmaking, officials said.
"I am neither a zealot nor an extremist," the general said in the statement. "Only a soldier who has an abiding faith."
Defense Secretary Donald H. Rumsfeld said Thursday he had not seen Boykin's comments, but he praised the three-star general as "an officer that has an outstanding record in the United States armed forces."
Despite repeated questions at a Pentagon press conference, Rumsfeld declined to condemn Boykin's statements or to say whether he would take any action.
A Muslim rights group, the Council on American-Islamic Relations, had called for Boykin to be reassigned from his job, which includes evaluating and providing resources for the intelligence needs of military commanders. Other religious freedom advocacy groups made similar statements.
"A man who sees the conduct of U.S. foreign policy as some sort of Christian religious crusade should not be making policy," said the Rev. Barry W. Lynn of Americans United for Separation of Church and State, an advocacy group.
The Bush administration has gone to some lengths to court Muslim organizations since the Sept. 11, 2001 attacks set off the U.S. war on terror. Muslim leaders have been invited to the White House, and President Bush declared late last year that Islam is a peaceful religion, seeking to distance himself from remarks by conservative Christian leaders Pat Robertson and the Rev. Jerry Falwell.
Boykin's statement echoed the president's past comments.
"I do believe that radical extremists have tried to use Islam as a cause for attacks on America," Boykin said. "As I have stated before, they are not true followers of Islam. In my view they are simply terrorists, much like the so-called 'Christians' of the white supremacy groups."