John Henry Browne said members of the defense team in Afghanistan were told they would have access to witnesses at a hospital, but later discovered the people had been released.
He also said the U.S. government has not turned over files to the lawyers defending Army Staff Sgt. Robert Bales.
The defense team said in a statement the prosecution is withholding information "while potential witnesses scatter."
"It's outrageous," Browne said. "What they are basically doing is hiding evidence. The only reason to hide evidence is if you don't have evidence."
Maj. Chris Ophardt, an Army spokesman, said in a statement that the prosecution will provide Bales' defense with evidence in accordance with court martial and military rules of evidence. He said within these guidelines "the prosecution is and has been communicating with the defense."
Defense Secretary Leon Panetta, after speaking to hundreds of Marines and sailors aboard the USS Peleliu off the coast of San Diego, told reporters: "I've made very clear that those procedures will be followed and that he'll be entitled to whatever information he would be entitled to under the military code of justice."
At a news conference Friday, Browne said the military is not under a legal obligation to provide his team with certain information at this point, but they were led to believe they'd have more assistance.
He said being given access to information at a later date won't work, especially in regards to witnesses in Afghanistan.
"Normally, we have cooperation with prosecutors and we get information, and in this case they actually promised us if we sent people to Afghanistan ... that they would cooperate," he said.
Browne also said the military planned to conduct a comprehensive mental health evaluation of Bales at the military prison at Fort Leavenworth, Kan.
Browne said the military initiated the evaluation and that it will take place within the next two months. He said it will likely delay the overall legal process involving Bales.
Bales has been charged with 17 counts of premeditated murder. The military says Bales left his base on southern Afghanistan and went on a nighttime shooting rampage through two villages on March 11.
The defense statement said the team in Afghanistan attempted to interview injured civilians being treated at a hospital in Kandahar, but were denied access and told to coordinate with prosecutors.
The prosecution team interviewed the civilians, but the defense team said they were unable to after the people were released and no contact information was provided for them.
Browne's team also said they have been denied access to the civilians' medical records, as well as video allegedly taken from a surveillance blimp showing Bales on the night of the killings.
Dan Conway, a military attorney who represented one of four Lewis-McChord soldiers convicted in the deliberate killings of three Afghan civilians in 2010, said the government doesn't appear to be doing anything wrong at this point in the Bales case. He said prosecutors have little obligation to turn over evidence right now and doesn't need to help coordinate interviews this early in the process.
"This is just going to be an uphill battle," Conway said.
The defense will have a right to interview witnesses that could be called at trial, so the Army could then take the defense team into the villages with security or coordinate to have them come onto the military base.
But Conway said the challenges of interviewing witnesses now means the defense team may not be able to track down people to bolster their case - such as witnesses unable to identify Bales or those who believe there were two shooters.
"If they want to talk to those witnesses, they're going to have to get an investigator and probably go to the village and talk to civilians themselves," Conway said.
U.S. military officials have said Bales was drinking on the base before creeping away to the villages, shooting his victims and setting many of them on fire. Nine were children.
Bales has had incidents involving alcohol and violence in the past. In 2002, he was arrested for a drunken assault of a security guard at a Tacoma casino. That charge was dismissed after Bales completed 20 hours of anger management training.
In 2008, a couple accused an intoxicated Bales of grabbing a woman's hand and thrusting it toward his crotch before kicking and punching the woman's boyfriend, according to a police report. Prosecutors declined to pursue that case.