By Jane Sutton

GUANTANAMO BAY U.S. NAVAL BASE, Cuba (Reuters) - U.S. prosecutors and defense attorneys for five defendants in the September 11 attacks dug in on Sunday for a long legal battle that one lawyer said may never be resolved.

The military tribunal is not expected to start for almost another year and if Saturday's 13-hour arraignment was an accurate preview, the trial will be chaotic and drawn out with continuing disputes about torture and whether a military trial is appropriate.

The defendants on Saturday refused to enter pleas and demanded a full reading of the charges against them. The proceeding was interrupted by outbursts from the defendants, one of whom stripped off his shirt to show scars.

The judge, Army Colonel James Pohl, set the next hearing for June 12 and said the trial will not start until at least mid-2013. Chief Prosecutor Army Brigadier General Mark Martins said at a Sunday news conference he was not discouraged by the slow pace.

"However long the journey ... the United States is committed to accountability under law for those who have plotted to attack our nation and to kill innocent people," he said.

Almost 3,000 people died in 2001 when operatives from Osama bin Laden's militant Islamic group al Qaeda flew hijacked airliners into the World Trade Center towers in New York, the Pentagon and a field in Pennsylvania.

Turning aside defense arguments the tribunals are illegitimate, Martins said that admitted September 11 mastermind Khalid Sheikh Mohammed and his co-defendants are being tried in a system endorsed by the U.S. Congress and two U.S. presidents.

Defense lawyer James Connell said the tribunals would be lengthy and may never come to a resolution.

"I just want to leave you with the idea that the arraignment yesterday demonstrates that this will be a long, hard-fought but peaceful struggle against secrecy, torture and the misguided institution of the military commissions," Connell said at the news conference.

The decision to move to trial in a military court is the latest chapter in a decade-long political and legal battle over handling detainees. One of the most contentious issues has been whether terrorism suspects should be tried in civilian courts as criminals or before military courts as enemy combatants.

Defense lawyers repeatedly have said the tribunals are a second-class system of justice that deprives the defendants of the rights guaranteed by the U.S. Constitution.

The defendants refused to answer the judge's questions during Saturday's hearing because they did not acknowledge the legitimacy of the tribunals, said Connell, a civilian lawyer for Mohammed's nephew, defendant Ali Abdul Aziz Ali.

All five defendants have said they were tortured while held in secret CIA custody and their lawyers said the abuse continued at Guantanamo, where they have been held since 2006.

"The treatment has had serious long-term effects and will ultimately infect every aspect of the military commission tribunal," Connell said.

The CIA has acknowledged water boarding Mohammed 183 times. Martins said the torture issue would be aired in court and that torture-tainted evidence would not be used. That does not mean the defendants, who could face the death penalty if convicted, should go free, he said.

"The remedy is not to just dismiss all charges," Martins said. "It's harder than that. You've got to look and see if there is independent evidence."

The five defendants originally were charged in the Guantanamo tribunals in 2008. The Obama administration halted the proceedings and tried to move the case into a federal court in New York but, under political pressure, filed new charges in Guantanamo. The defendants were arraigned Saturday on the refiled charges.

The Islamic militant defendants are accused of conspiring with bin Laden and the plane hijackers, murder in violation of the laws of war, hijacking, terrorism and other charges stemming from the 2001 attacks that propelled the United States into a global war against al Qaeda and its supporters.

(Editing by Michael Connor and Bill Trott)