The judge presiding over the prosecution of alleged WikiLeaks source Bradley Manning has ruled that the US soldier was brought to trial in good time and did not have his constitutional rights violated, removing the final impediments to a full court martial trial in June.

The ruling dashes the defence team's hopes of having the charges against Manning dismissed. His lead lawyer, David Coombs, had argued in legal argument to the court that "extreme foot-dragging" by the prosecution had violated the accused's right to a speedy trial.

The judge, Colonel Denise Lind, spent two hours reading out her judgement to a pre-trial hearing in Fort Meade, Maryland. She went through the procedures in preparing for trial in minute detail, concluding that the exceptional length of the case was almost entirely justified as a result of its uniquely complex and sensitive nature.

The question of how long the WikiLeaks source has been held in prison has become a hot-button issue in the case. Hundreds of demonstrators gathered in 70 locations around the world last Saturday to protest the 1,000th day Manning has been in military custody without trial.

But in her deliberations on the number of days it had taken to bring Manning to trial, the judge was dismissive of the defence arguments. The soldier, who has admitted to having transferred state documents to the anti-secrecy website WikiLeaks, was officially put into pre-trial confinement on 28 May 2010 when he was arrested at a forward operating base outside Baghdad.

Under the Rules of Court Martial 707, any member of the military who is prosecuted must be brought to trial – as measured by the date of his or her arraignment – within a "speedy trial clock" of 120 days of being detained. But there are grounds for excusable delays that set back the clock that include the need for counsel to prepare for trial in a complex case, an inquiry into the mental condition of the accused, and the time taken to obtain security clearance for classified information.

In Manning's case, the defence and prosecution agreed that there had been 84 days of diligent work between the soldier's arrest and his arraignment on 23 February 2012. But the two sides were in dispute over 330 days.

In her ruling, Lind found that only six of those 330 days had been improperly excluded form the speedy trial clock – in other words, almost all the delays had been justified. She said the length of the delay was "reasonable under the unique circumstances of this case", adding that the government had worked "diligently" in a case burdened by "voluminous information".

The judge went as far as to praise the prosecution for having set up a "systematic approach" to advance the case through a succession of monthly updates related to the preparation of classified material for disclosure to the defence. "That should be encouraged given a case like this with such voluminous information. There was a good cause for the reasonable delay."

Lind also dismissed a defence claim that Manning's rights had been violated under the sixth amendment of the US constitution and article 10 of the Uniform Code of Military Justice that also protect individuals against an unjustifiably lengthy trial.

The ruling clashes with the approach taken by Manning's defence team. Coombs has protested repeatedly during the course of the proceedings that the process was being dragged out by the US government, accusing the prosecution of "shameful" lack of diligence in moving speedily to trial.

Tuesday's judgment means that the soldier is now almost certain to go to trial for the transmission of hundreds of thousands of US diplomatic cables, intelligence memos and videos to WikiLeaks. The trial is currently set to begin on 3 June and is scheduled to last 12 weeks, Lind said.

A panel of the court martial – equivalent to a jury in a civilian trial – has already been assembled and instructed not to read or watch any media reports relating to the trial or to WikiLeaks. Manning has indicated, however, that he intends to be tried by judge alone without the presence of a panel of his peers.

Lind spent an hour reading out her ruling, stopping only to drink from a bottle of water. The judgement is not being made available to the public, further exacerbating complaints that the trial is being conducted amid excessive secrecy.