Robert Mueller/file fbi photo

Mr. Mueller’s comments are the first indicating that the joint House-Senate conference bill failed to resolve concerns that had prompted the Obama administration to threaten to veto the legislation.

The legislation requires military custody of terrorism suspects who are members of al Qaeda and affiliated groups. In response to White House concerns, lawmakers included a provision to give the president broad discretion over whether the military or the civilian justice system takes the lead in terrorism investigations.

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