The judge scheduled courts-martial next month for Petty Officer 2nd Class Matthew McCabe of Perrysburg, Ohio, and Petty Officer 1st Class Julio Huertas of Blue Island, Ill. A third SEAL will be arraigned later.
The SEALs have received an outpouring of public support on the Internet, and a California congressman has led a campaign urging Defense Secretary Robert Gates to intervene. About three dozen protesters, including the mother of one of the slain contractors, stood outside the Norfolk Naval Station gate Monday morning holding signs of support.
McCabe is accused of striking the detainee in the midsection, dereliction of duty for failing to safeguard the detainee, and lying to investigators. He deferred entering a plea until his Jan. 19 trial.
McCabe told reporters he was confident he would be exonerated.
"I feel very good about it," he said as he made his way through the crowd of supporters, shaking hands and thanking them. "The support is phenomenal. It makes us feel better, all these people being behind us."
Huertas pleaded not guilty to charges of dereliction of duty, lying to investigators and impeding an investigation. His trial was set for Jan. 11.
"He's been a hero - two tours of Iraq and one tour of Afghanistan - and now this is the thanks he gets," Huertas' civilian attorney, Monica Lombardi, told reporters after the arraignment.
Military attorneys were not available for comment.
McCabe and Huertas both deferred a decision on whether to be tried by a military judge or jury. Lombardi said they couldn't choose because they still have not received the prosecution's evidence.
The men could have accepted a nonjudicial reprimand but wanted to go to trial to clear their names, Lombardi said. A reprimand could have resulted in a loss of rank; if they are convicted at trial, they could get up to a year in jail, a bad conduct discharge, or a loss of rank or pay.
McCabe declined to talk to reporters about specifics of the case. His father, Marty McCabe of Las Vegas, said all his son did was his job.
"It just turns my stomach to have these people send him over there and put him in harm's way, and then they don't have his back when he gets home," Marty McCabe said.
Military officials have cautioned against a public rush to judgment, saying a true picture will emerge when all the evidence is heard. However, more than 45,000 people have signed onto a Facebook page supporting the SEALs, and U.S. Rep. Duncan Hunter, R-Calif., said in a letter to Gates last week that the prosecution was an overreaction by the military.
The charges stem from an alleged assault after the SEALs captured Ahmed Hashim Abed in early September. Abed is believed to be connected to the killings of four Blackwater security guards who were protecting a convoy when they were attacked by Iraqi insurgents. Their burned corpses were dragged through the city, and two of them were hung from a bridge over the Euphrates River.
Donna Zovko of Cleveland, whose son Jerry Zovko was among the slain contractors, said the prosecution of the SEALs who captured Abed was "very heartbreaking."
"For these young Navy SEALs, I am very thankful and hopeful that they will be OK," Zovko said.
Along with McCabe and Huertas, Petty Officer Jonathan Keefe of Yorktown, Va., is charged with dereliction of duty and making a false official statement. His arraignment has not been scheduled.
The SEALs, based at Joint Expeditionary Base Little Creek in Norfolk, are not in custody.