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WASHINGTON — In transferring a Somali terrorism suspect to federal court after two months of interrogation aboard a U.S. Navy ship, the Obama administration is crafting a detention policy that blends civilian and military options for handling captured foreign militants.

Administration officials insisted that in this case, the federal criminal code offered a better way to charge the suspect than laws enforced by a military commission. But the Somali’s secret transfer to New York also appeared to challenge Congress, where lawmakers are trying to prevent just that option.

Ahmed Adulkadir Warsame, an alleged liaison between two al-Qaeda affiliates — Somalia- based al-Shabab and Yemen- based al-Qaeda in the Arabian Peninsula, or AQAP — was captured on a boat in the Gulf of Aden in April and held on a U.S. Navy ship for interrogation until he was flown to the United States this week for prosecution in civilian court.

“Wherever possible, our first priority is and always has been to apprehend terrorist suspects and to preserve the opportunity to elicit valuable intelligence that can help us protect the American people,” White House spokesman Jay Carney said Wednesday. “In this case, the government . . . has been able to acquire very valuable intelligence from this operation.”

A U.S. official described Warsame as a “senior commander for al-Shabab” and said there was “strong reason to believe” that he was in contact with U.S.-born Anwar al-Aulaqi, a top AQAP figure, during time that Warsame spent in Yemen.

The administration’s marriage of two systems in the case — relatively unimpeded military detention followed by a traditional criminal prosecution — immediately drew fire from Republicans and the civil liberties community.

Backed by numerous Democrats on Capitol Hill, Republicans are pressing legislation that would compel the administration to transfer all terrorism suspects to Guantanamo Bay, Cuba, for indefinite detention or trial by military commission.

The American Civil Liberties Union and Amnesty International criticized the Somali’s extended detention aboard a military vessel, where he was subjected to almost-daily questioning without a lawyer.

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