Ghailani, a native of Tanzania, was sent to New York for prosecution in June 2009 in what the Obama administration hoped would be the first case in a series of federal prosecutions of Guantanamo detainees, including Khalid Sheik Mohammed and four co-conspirators accused of organizing the Sept. 11, 2001, attacks.

That plan has run into fierce, cross-party opposition in Congress and New York. The failure to convict Ghailani on the most serious terrorism charges will bolster the arguments of those who say that the military prison at Guantanamo Bay should be kept open, both to host military commissions for some prisoners and hold others indefinitely under the laws of war.

Ghailani still could be sentenced to life in prison, and faces a minimum of 20 years, according to the Justice Department. But the verdict was a blow to administration officials who were quietly confident that Ghailani would be found guilty on all charges, despite the judge’s ruling against the government on a key issue. Just last week, a senior administration official said a not guilty verdict would be a « disaster » for the administration’s Guantanamo policy.