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The government’s new system for trying Guantanamo detainees was thrown into turmoil Monday after military judges in separate decisions dismissed war crimes charges against two of the detainees.

The rulings, the latest legal setbacks for the government’s effort to bring war crimes charges against detainees, could stall the military’s prosecutions here.

The decisions did not turn on the guilt or innocence of the detainees, but rather made essentially the same determination that the military hadn’t followed procedures in declaring the detainees “unlawful enemy combatants,” which is required for the military commission to hear the cases.

Pentagon officials described the rulings as raising technical and semantic issues, and said they were considering appeals. If appeals failed, they said, they could go through the process of redesignating the detainees.

But military lawyers said the rulings exposed a flaw that would affect every other potential war crimes case at Guantanamo. The rulings also brought immediate calls, including from some on Capitol Hill, for Congress to re-examine the system it set up last year for military commission trials.

Monday’s rulings came in the cases of the only Canadian detainee, Omar Khadr, and a Yemeni, Salim Ahmed Hamdan, who is accused of being an Al Qaeda driver for Osama bin Laden.

Hamdan’s appeal of a prior effort to prosecute him led to a Supreme Court decision last June in which the justices struck down the administration’s first system for war crimes trials. The military judge in Hamdan’s case, Navy Capt. Keith Allred, said the Pentagon had failed to obtain the necessary enemy combat- ant classification.

Hamdan’s military lawyer, Lt. Cmdr. Charles Swift, said that though his client is unlikely to obtain freedom because of the decision, “it was once again a victory for the rule of law.”

The judge in Khadr’s case, Army Col. Peter Brownback, said that because the detainee hadn’t been declared an unlawful enemy combatant, the military court lacked jurisdiction and the case couldn’t continue.

“A person has a right to be tried only by a court which he knows has jurisdiction over him,” Brownback said from the bench in the military courtroom here.

Sen. Arlen Specter (R-Pa.), the senior Republican on the Judiciary Committee, said the decision raised significant issues and could prompt Congress to re-evaluate the legal rights of detainees, including Congress’ decision last year to revoke the rights of detainees to file habeas corpus suits to challenge their detentions.

“The sense I have is that there’s an unease, an uncomfortable sense about the whole Guantanamo milieu,” Specter said, adding, “There’s just a sense of too many shortcuts in the whole process.”

Whatever the ultimate legal ramifications of Monday’s rulings, they are another in a string of unexpected detours in the government’s 5-year effort to establish a special legal system for trying foreign terrorism suspects. The current commission system was approved by Congress after the Supreme Court last June struck down the administration’s first plan for holding war crimes trials.

The military judges said Congress authorized bringing war crimes charges against detainees who had been declared by military tribunals to be “unlawful enemy combatants.”

But they said the tribunals held at Guantanamo, known as combatant status review tribunals, had determined only that the detainees were enemy combatants without making the added determination that their participation was “unlawful.”

The international law of war defines unlawful combatants as fighters who, for example, do not wear military uniforms and conceal their weapons.

Khadr, who was 15 when he was captured in Afghanistan, is charged with killing an American soldier, spying, supporting terrorism and other charges.

The White House declined to comment on the decisions.

Army Maj. Beth Kubala, spokeswoman for the Pentagon’s Office of Military Commissions, said the day’s rulings demonstrated that the military judges operate independently.

But she suggested that the military doesn’t view the rulings as paralyzing to its prosecutions for alleged war crimes.

“The public should make no assumptions,” Kubala said, “about the future of military commissions.”

A Pentagon statement said: “We believe that Congress intended to grant jurisdiction under the Military Commissions Act to individuals, like Mr. Khadr, who are being held as enemy combatants.”

But Specter said it was “dead wrong” for anyone to assert that Congress intended to permit prosecution of detainees who had not been declared unlawful enemy combatants.

So far, three detainees have been charged with war crimes under the law passed last year, including Khadr and Hamdan.

The third detainee, David Hicks, pleaded guilty earlier this year and was sent to his native Australia. Prosecutors have said they may file such war crimes charges against about 80 of the 380 detainees at Guantanamo.

Under directives from President Bush and senior Defense Department officials, military officials here have held detainees after finding simply that they were “enemy combatants.”

Those procedures have long drawn criticism, with some opponents of administration policies saying they appeared to ignore principles of the international law of war.

The military could repair the problem raised by the military judges on Monday by holding new combatant status review hearings to determine whether each of the detainees slated for war crimes charges was an unlawful combatant.

Some experts on military law said the new tangle of legal challenges would almost certainly cause extensive delays.

David Glazier, a retired Navy commander who is an associate professor at the Loyola Law School in Los Angeles, said, “All the individuals that the government wants to charge will have to go through the [tribunal] process again.