WASHINGTON (AP) -- After a bruising battle in Congress, the Obama administration retained the right to investigate and try suspected terrorists in civilian courts. But officials say newly enacted legislation raises a host of questions that will complicate and could harm the investigation of terrorism cases.
During a struggle that began last May and ended this past week in a compromise defense bill, the administration waged an uphill fight against a majority of Republicans and some Democrats trying to expand the role of the military while reducing the role of civilian courts in the fight against terrorism.
It was the latest effort by conservatives to keep open the U.S. military prison facility at Guantanamo Bay, Cuba, to place terrorism suspects in indefinite detention and to designate military commissions as the preferred alternative to civilian courts for meting out justice.
In the end, the administration came away with one major victory. Gone from the defense bill during House-Senate negotiations was a provision that would have eliminated executive branch authority to use civilian courts for trying terrorism cases against foreign nationals.
The new law would require military custody for any suspect who is a member of al-Qaida or "associated forces" and involved in planning or attempting to carry out an attack on the United States or its coalition partners. The military custody requirement does not apply to U.S. citizens or to lawful U.S. residents.
The president or a designated subordinate may waive the military custody requirement by certifying to Congress that such a move is in the interest of national security.
The new law "will ramp up the political costs" when the administration decides to hold a civilian criminal prosecution for a detainee, said University of Texas law professor Robert M. Chesney, who focused on detainee issues while serving at the Justice Department in 2009.
But, Chesney added, "this law does leave the president with flexibility" to have civilian trials "and therefore the law is neither quite as bad as its opponents say nor as useful as its supporters think."
Weighing in heavily in the debate was the FBI, the front-line investigative agency that now must operate in a reordered environment in which the U.S. military will suddenly play a bigger role that is sometimes side by side with law enforcement.
In a Nov. 28 letter to Congress, FBI Director Robert Mueller said the legislation will inhibit the bureau's ability to persuade suspected terrorists to cooperate immediately and provide critical intelligence.
Mueller tried to make a similar point at a Senate Judiciary Committee hearing this past week, but got little sympathy from Sen. Jeff Sessions, R-Ala.
"What I am focused on is what happens at the time of arrest," the FBI director said.
"Well, then you need to work this out with the Department of Defense, don't you?" said Sessions, a former federal prosecutor and ex-Alabama attorney general.
Mueller also said it wasn't clear how agents should operate if they arrest someone covered by the military custody requirement but the nearest military facility is hundreds of miles away.
And last month, Lisa Monaco, assistant attorney general for national security, said that "agents and prosecutors should not have to spend their time worrying about citizenship status and whether and how to get a waiver . in order to thwart an al-Qaida plot against the homeland."
Law enforcement officials, speaking on condition of anonymity because they are not authorized to speak publicly about the matter, say that it won't be easy working under a new set of rules that must be written in the next 60 days before the law goes into effect.
Pressure from the administration produced one late compromise section that says nothing in the bill may be "construed to affect the existing criminal enforcement and national security authorities of the Federal Bureau of Investigation or any other domestic law enforcement agency with regard to a covered person, regardless whether such covered person is held in military custody."
But that left open questions.
"I'm concerned with the lack of clarity about who is in charge of investigation and interrogation for detainees in military custody," Michael J. Nardotti, the judge advocate general of the Army from 1993 to 1997, said of the legislation.
"If the detainees are in military custody and the military is responsible for their disposition and control, what role does the FBI have in that process and is the FBI going to be directed in some respects by the military on the use of the bureau's investigative resources?" asked Nardotti.
"The second concern I have," said Nardotti, "is that the use of the words 'associated forces' in the legislation can be read as expanding the definition of who can be held indefinitely in military custody in an open-ended conflict." That could become an important issue because the legislation will undoubtedly at some point -- or at many points -- undergo scrutiny by the courts.
Gary Solis, a retired judge advocate who served 26 years in the Marine Corps, called the latest political venture into how best to battle terrorism "a very bad idea."
"Making the military the warders of every suspected terrorist goes far beyond the military's legislatively assigned mission," he said.
"It appears to me to be an effort to assure that all suspected terrorists will be tried by military commission," said Solis. "Despite the fact that hundreds of terrorists have been tried in the federal courts, convicted and sentenced to long terms, for reasons that escape me Congress is unwilling to allow our courts to proceed with what they have demonstrably been so capable of doing."
Congress and the White House have been at odds over detention policy ever since President Barack Obama was sworn in.
Many lawmakers have resisted the administration's efforts to close the U.S. prison at Guantanamo Bay and have opposed trying terror suspects in federal courts in the United States rather than by military commission. This latest round featured some Democrats, including Senate Armed Services Committee chairman Carl Levin of Michigan and Sen. Daniel Inouye of Hawaii, supporting the measure while some Republicans and libertarian-leaning Republicans, including Rand Paul of Kentucky and Mike Lee of Utah, opposed the legislation that the administration objected to.
Associated Press writer Donna Cassata contributed to this report.