By James Vicini WASHINGTON, Feb 9 (Reuters) - An American citizen who has been held by U.S. military forces in Iraq for more than two years cannot be transferred to Iraqi authorities for trial on terrorism charges, a federal appeals court ruled on Friday. The 2-1 ruling by the appellate panel was a major defeat for the Bush administration, which had argued that U.S. courts have no authority to stop the military from transferring an American citizen to an Iraqi court. Shawqi Omar, a dual U.S.-Jordanian citizen, was captured at his Baghdad home in October 2004 in a raid targeting associates of al Qaeda's former leader in Iraq. Omar, who is being held at Camp Cropper near Baghdad airport, says he has been in custody for more than two years without formal charges and without access to a lawyer. In response to a request by Omar's American wife and son in the United States, a federal judge here a year ago issued a preliminary injunction barring Omar's transfer to Iraqi custody. The appeals court upheld that ruling. The lawsuit filed on his behalf expressed concern that Omar might be tortured or even killed if he were transferred to Iraqi custody. Omar, who became a U.S. citizen after his 1986 marriage, says he went to Iraq after the overthrow of Saddam Hussein's government seeking reconstruction-related work. The U.S. military says he was part of the network of Abu Musab al-Zarqawi, al Qaeda's former leader in Iraq, and he facilitated terrorist activities inside and outside of Iraq. It says weapons and bomb-making materials were found in his home. The lawsuit said his detention by the U.S. military violates his U.S. constitutional rights, federal law, Army regulations and international law. The lawsuit said the U.S. military lacks the authorization to transfer him to Iraqi authorities and that the U.S. Constitution forbids his transfer to a government likely to torture him. ADMINISTRATION REBUFFED The opinion written by Judge David Tatel rejected the Bush administration's arguments that U.S. courts here lack jurisdiction over the case. "The government concedes Omar is in the custody of United States officials, and Omar's petition merely calls on the district court to determine whether those officials are complying with American law -- an altogether unremarkable action for a United States district court," he wrote. Tatel rejected the administration's arguments that U.S. courts lack jurisdiction because the case involved foreign policy or military issues that are beyond the judiciary's authority or competence to answer. Judge Janice Rogers Brown dissented and said she would set aside the injunction. "The majority's holding has the remarkable effect of enabling a court sitting in Washington, D.C., to block the efforts of a foreign sovereign to make an arrest on its own soil," she wrote. "Omar has not established any legal basis for protection from Iraqi custody." A spokesman said the Justice Department was disappointed with the ruling and agreed with Judge Brown that it would interfere with the U.S. military's power to conduct a war.