Colonel Denise Lind, presiding over the trial of Bradley Manning, will not throw out the most serious charge against him - that he 'aided the enemy'.
Manning's defence urged Lind to dismiss the notion he knowingly aided the enemy. If found guilty, Manning could spend life in prison without parole.
The leak was the biggest ever of secret US documents.
Prosecutors argued Manning had "systematically harvested" documents, which were eventually seen by Osama bin Laden. They also say the leaks have damaged national security and put American lives at risk, although critics dismiss this argument as dishonest and spurious.
Critics such as the Bradley Manning Support Network suggest that it is the United States administration itself that has threatened national security with its interventionalist policies of aggression abroad, not to mention Obama's drone assassination campaign which has actually killed an American.
Manning has already pleaded guilty to 10 charges which could see him imprisoned for up to 20 years, however, the United States is seeking punishment of up to 154 years plus the maximum life sentence for "aiding the enemy".
"He [Pte Manning] was knowingly providing intelligence to the enemy," Judge Colonel Denise Lind said during the Fort Meade, Maryland hearing, the BBC reports.
A key witness, Colonel Morris Davis, who was director of the US air force's judigicial system from 2007-2008, said he was "extraordinarily disappointed" by the decision. Ordinarily, Davis defends military justice, but he expressed concern about the extent of Manning's heavy-handed prosecution. Davis compared the Manning trial to the marines who faced courtmartial over the 2005 Haditha killings.
In Haditha, 24 unarmed Iraqis were murdered by US marines. Six of the marines had the case dropped, another was found not guilty, and only one defendent was convicted of a single count - but still avoided jail time.
Davis said the difference between the responses suggest the military justice system "is not working".
Human rights advocacy group Amnesty International, the Guardian reports, called the decision a travesty of justice. "It's abundantly clear that the charge of 'aiding the enemy has no basis and the charge should be withdrawn," senior director for international law, Widney Brown, said.
Manning, his defence team earlier said, was young, naive and good intentioned when he arrived in Iraq. But his growing disillusion spurred him to allegedly leak the documents.
Civilian lawyer for Manning, David Coombs, claimed the US govnment hadn't provided any substantial evidence that Manning knew he was providing information to enemies of the United States. Coombs argued if he was found guilty of "aiding the enemy" this would set a dangerous precedent for all whistleblowers and the freedom of the press.
Manning's trial is bound up with the Obama administration's increasingly restrictive and authoritarian stance on whistleblowers and the press.
A global manhunt is underway for Edward Snowden for revealing the NSA's worldwide spying programme. The US government has attempted to paint him as a 'leaker' and of a collaborator with foreign interests hostile to America. Despite this, the American public broadly supports Snowden, a public opinion survey found.
Earlier this year the Associated Press, meanwhile, claimed the Justice Department secretly obtained two months of reporter and editor telephone records. The organisation's top executive called it a "massive and unprecedented intrusion" into how news is gathered.