The US government is planning to call 141 witnesses to the trial of Bradley Manning, including 15 people who would testify that the information he passed to WikiLeaks caused harm to US national interests.

The gigantic scale of the prosecution plans was revealed during pre-trial legal argument over how sensitive secret information would be handled. The trial, scheduled to start on 3 June and pencilled in for 12 weeks, is the most prominent prosecution of the source of an official leak for at least a generation.

Ashden Fein, the leading prosecution counsel, told the court that four witnesses would be called whose testimony would have to be given anonymously and entirely behind closed doors, with only the judge, case lawyers and the accused present. One of the four would be "John Doe", the probable US Navy Seal involved in the killing of Osama bin Laden.

In addition, 33 witnesses would have sensitive or secret information to impart to the court, Fein said, and should therefore be heard partially in closed session. Fein said that the witnesses would discuss matters such as "injury and death to individuals" accruing from the WikiLeaks disclosures, and how "capability of the enemy increased in certain countries".

He gave the hypothetical example of testimony relating to a US soldier who had been killed from a roadside bomb. The witness might relate that the IED had been planted in a particular location using intelligence gleaned from a report published by WikiLeaks.

The question of how much, if any, damage to US interests was caused by the WikiLeaks revelations in 2009-2010 has been a matter of heated debate ever since. Hillary Clinton, then secretary of state, called the disclosures an "attack on America's foreign policy interests" that "tears at the fabric" of responsible government.

But State Department officials told Reuters in 2011 that the 250,000 diplomatic cables published by WikiLeaks were more embarrassing than damaging.

David Coombs, Manning's chief defence lawyer, objected to the prosecution's suggestion that all of its 33 sensitive witnesses should be allowed to give some evidence in closed session and some in open court. He said that was too vague, and counter-proposed that the court should decide on a witness-by-witness basis.

The judge presiding over the case, Colonel Denise Lind, will be holding a private discussion with both legal sides to decide how to proceed.

Earlier in the day, Lind gave her ruling over the defence team's proposal to argue at trial that Manning's impact in leaking to WikiLeaks was minimised by the fact that the US is guilty of general over-classification of information. The defence has indicated that it intends to call witnesses, and present evidence to court, that shows that the system of classification is broken, and that the state is excessively secretive in its handling of information.

The issue of excessive secrecy has also become a talking point in Washington in recent times. In October 2010 President Obama signed into law the Reducing Over-Classification Act designed to rationalise state secrets.

Despite the new law, the advisory committee to Congress on this issue reported in December that the classification system remained "outmoded and unsustainable".

In her ruling, Lind denied Manning the right to present evidence at his trial that the US government is guilty of excessive secrecy. She said that the soldier had no authorisation within the army to determine whether a document was correctly or incorrectly classified – that was the job of trained government officials working in the "original classification authorities" or OCA.

"There is no nexus between general over-classification and the information allegedly communicated in this case," Lind said.

She rejected most of Manning's desired witnesses and evidence during the prosecution phase of the trial. He would be allowed only to call one witness – William Leonard of the National Archives and Records Administration – and to refer to the Reducing Over-Classification Act.

At sentencing, he might be allowed to present evidence of over-classification in mitigation in an attempt to reduce the punishment. But Lind said she would rule on that matter when the time comes.

• This article was amended on 28 February 2013 to add the words "that the US government is guilty of excessive secrecy" to the subheading, to clarify its meaning.