The judge presiding over the court martial of the WikiLeaks source Bradley Manning has declined to throw out the main charge against him - that he knowingly "aided the enemy" by leaking state secrets that were posted on the internet.

The decision by Colonel Denise Lind, who is sitting as judge and jury over the army private in a courtroom at Fort Meade, Maryland, means that Manning continues to face the possibility of life in military custody with no chance of parole. The "aiding the enemy" charge is one of the most severe offences available to military prosecutors, and has led to the accusation that the Obama administration is attempting to put a chill on whistleblowers that could have far-reaching consequences for investigative journalism.

Colonel Morris Davis, one of the key witnesses called by Manning's defence team in an attempt to have the "aiding the enemy" charge dropped, said he was "extraordinarily disappointed" by the ruling. Davis was director of the US air force's judicial system from 2007 to 2008 and said he was normally a defender of military justice.

But he said the fact that military prosecutors were pursuing Manning with such a heavy hand had forced him to think again. He pointed to the contrast between the full-blooded prosecution of the US soldier and the outcome of the court martial that flowed from the 2005 Haditha killings in Iraq.

In that incident, 24 unarmed Iraqis including women and children were killed by US marines. In the ensuing prosecutions, six of the marines involved had their cases dropped, a seventh was found not guilty and the only one to be convicted of a single count avoided any time in jail.

"When you think about these different responses, it suggests to me that the military justice system is not working," Davis said.

The defence team, led by a civilian lawyer, David Coombs, had moved for the "aiding the enemy" charge to be dismissed on grounds of lack of evidence. The motion argued that the US government had failed to produce any substantial evidence that Manning had "actual knowledge" that by passing documents to WikiLeaks he was giving information to an enemy of the US.

Coombs said that in the course of five weeks of prosecution evidence during the trial, the government had not proffered any evidence that the soldier was trained to be wary of WikiLeaks as a possible conduit to enemy groups. On the contrary, the court had heard from one of Manning's superiors who had trained him as an intelligence analyst who testified that he had never even heard of WikiLeaks prior to the soldier's arrest in this case.

To find Manning guilty of "aiding the enemy" would set an "extremely bad precedent" that would have an impact on all whistleblowers seeking to sound the alarm about government misconduct through established news outlets, Coombs later argued in court.

The prosecution countered that Manning had been thoroughly trained to recognise that posting any intelligence on the internet would make it accessible to enemy groups, particularly al-Qaida and its affiliated networks. "PFC Manning is distinct from an infantryman or a truck driver, because he had all the training. And this was his job. He knew exactly the consequences of his actions," one of the prosecutors, Captain Angel Overgaard, told the court.

On more than one occasion, the US government made clear that it would have treated Manning with an equally stern hand had he chosen to leak the information to the New York Times rather than WikiLeaks. The issue was not purely legalistic – in the course of pre-trial hearings Manning indicated that his first attempt at linking to a news organisation was to the New York Times, Washington Post and Politico but he had failed to make contact and as a result had turned instead to WikiLeaks.

Amnesty International said that Lind's decision to keep "aiding the enemy" on the charge sheet was a travesty of justice. "It's abundantly clear that the charge of 'aiding the enemy' has no basis and the charge should be withdrawn," said the human rights group's senior director for international law, Widney Brown.

Steven Aftergood, who heads a project on government secrecy at the Federation of American Scientists, called Lind's ruling "sobering". He added: "It's disturbing though not altogether surprising."

Aftergood said that Manning was suffering the consequences of what he called an "indiscriminate release of records. I can't believe that if he had simply released the Apache helicopter video or some of the other specific documents he transmitted that he would be facing the same set of charges."

Manning has admitted to 10 lesser included offences relating to the leaking of hundreds of thousands of US state secrets that included war logs from Afghanistan and Iraq, detainee files from Guantánamo, a video of the Apache helicopter attack on civilians in Baghdad and a huge trove of US diplomatic cables. The offences to which the soldier has pleaded guilty carry an upper sentence of 20 years, though the US government is seeking a more serious punishment that would see him languish in jail for up to 154 years in addition to the maximum life sentence for "aiding the enemy".

The judge is expected to deliver her verdict on all 21 counts pursued by the government, as well as the 10 lesser offences admitted by Manning, possibly as early as next week.