WASHINGTON  Attorney General Eric H. Holder Jr. on Wednesday defended his decision to prosecute five men accused as co-conspirators in the Sept. 11 attacks in federal court in Manhattan, declaring that while he believes “we are at war,” that the venue was the best place to pursue the case against them.

Despite criticism that holding such a trial presented greater risks than a military commission, Mr. Holder argued that there were fewer differences between the rules for federal court and the military panels than some critics realize. And, he argued, the Southern District of New York has a long history of successfully prosecuting terrorism suspects.

“We need not cower in the face of this enemy,” Mr. Holder said, testifying before the Senate Judiciary Committee. “Our institutions are strong, our infrastructure is ready, our resolve is firm, and our people are ready.”

But Senator Jeff Sessions of Alabama, the ranking Republican, objected to characterization of opposition as cowardice. He argued that there were strong reasons to prosecute the accused, including Khalid Shaikh Mohammed, the self-described mastermind of the Sept. 11 attacks, before a military court.