Ahmed Abdulkadir Warsame, believed to be in his mid-20s, appeared before Southern District Judge Colleen McMahon in a case that could mark another chapter in the long fight over whether accused terrorists apprehended overseas should be tried in U.S. civilian courts.

Mr. Warsame was captured in the Horn of Africa region by U.S. military personnel on April 19 and questioned for intelligence purposes for over two months aboard a U.S. Navy ship. Senior administration officials said Tuesday night that he provided important intelligence on two State Department-designated terror groups—al-Qaida and its Somali ally, al-Shabaab—before being read his Miranda rights, waiving them and submitting for several days to questioning by FBI agents designed to elicit statements that could be used against him in his civilian trial.