Spokesman for US forces in Afghanistan, Col Dave Lapan, says the Afghan panel "exceeded its mandate" in ordering the release of 650 detainees from Parwan Detention Facility earlier this week.
Already, 562 of the prisoners have been freed while the 88 the United States has issues with remain behind bars.
Lapan said on Wednesday that the 88 "are legitimate threats for whom there is strong evidence supporting prosecution or further investigation."