Mukasey's remarks came amid fresh criticism of the legal processes at Guantanamo Bay. Just this week, the Pentagon defended the abrupt removal of a judge from a case after rulings unfavorable to the government.
Speaking to an annual conference of Washington federal judges, Mukasey said the decision to try terrorism cases outside of civilian courthouses is not made lightly.
"Our nation and our Constitution are never put in a more flattering light than when we prosecute in federal court those who have sworn to kill us," he said.
But Mukasey, a former federal judge, said that is not always possible. Criminal cases, he said, could jeopardize military operations and national security by forcing prosecutors to turn over sensitive intelligence data to lawyers for suspected terrorists.
"Different situations call for different solutions," he said.
As Mukasey was speaking, Human Rights Watch urged the government to move the trials of Khalid Sheikh Mohammed and four others accused in the Sept. 11 attacks from Guantanamo Bay to federal court. The five men are scheduled make their first appearance before a military judge on Thursday.
In civilian courts, hearsay evidence and confessions obtained through coercion are not admissible. Such evidence is allowed in the military commissions.
"The military commission trials, set to begin in the coming months, will look and feel a lot like federal trials, albeit with some important differences," Mukasey said.
But lawyers for Canadian detainee Omar Khadr questioned the integrity of the process recently after the Pentagon removed a judge, Col. Peter Brownback, who had issued rulings favorable to the defense.
"Whatever the case, this seriously undermines whatever integrity these proceedings possessed before," said Khadr's lawyer, Navy Lt. Cmdr. William Kuebler.
The Pentagon said Brownback was replaced because his service orders were expiring.
Mukasey also spoke about recent terrorism cases prosecuted in federal court, where the Justice Department had some high-profile setbacks. For example, a second prosecution against men accused of plotting to destroy Chicago's Sears Tower ended in a mistrial.
Federal prosecutors have said the violent threats allegedly made by the ringleader required another trial to "safeguard the community."
But there is no evidence the men ever acquired any explosives, building blueprints or other items needed to pull off an attack.
Mukasey did not mention the case specifically. But he rejected the idea that prosecutors have brought cases prematurely involving fanciful plots or tough talk. Rather than waiting to gather the evidence to bring the perfect case, he said prosecutors move quickly to disrupt such plots. That means the Justice Department will not prevail every time, he said.
"Are there any words that would comfort you if one of your loved ones were killed in a plot that the FBI dismissed as fanciful?" Mukasey said.
After all, he added, the idea that a group of men armed only with box cutters could take down the World Trade Center would have seemed fanciful on Sept. 10, 2001.