Military lawyers tell last hearing before trial they have dropped one of 22 counts but will still press most serious accusation

Prosecutors in the case against the WikiLeaks source Bradley Manning have decided to drop one of 22 counts against him, but are pressing ahead with the most serious accusation, that he "aided the enemy".

Military lawyers told Manning's final pre-trial hearing that they would no longer seek to prove the US soldier was guilty of leaking a single state department cable, known as "Reykjavik-13". The cable, which relates to the Icelandic financial crisis, was the first of a massive stash of diplomatic cables leaked by Manning to be published by WikiLeaks, on 18 February 2010.

Manning has been in military custody since May 2010, when he was arrested at a US military base in Iraq, where he was working as an intelligence analyst. He has pleaded guilty to a lesser offence relating to the leak of Reykjavik-13 and liable to a maximum of two years. The US government had sought to press further statutory charges on him that would have added up to an additional eight years on his sentence, but has now dropped the count.

It is not clear why government lawyers opted to remove the Reykjavik-13 count, though in the wider picture the move is of limited significance. If Manning is found guilty of "aiding the enemy" – in effect, assisting Osama bin Laden by making public information that could injure the US – he faces a possible life sentence with no chance of parole.

Should Manning be found not guilty to having aided the enemy, he still faces a further 20 counts carrying an overall maximum sentence of more than 150 years. At a minimum, the soldier has already pleaded guilty to lesser charges, of prejudicing the good order and discipline of the military by leaking information, which carry a maximum sentence of 20 years.

Among the counts that the government intends still to press is a sample group of more than 75 classified diplomatic cables drawn from the 250,000 or so that Manning has admitted transmitting to WikiLeaks. The government accuses Manning of leaking the embassy cables despite having reason to believe that they could be used to the injury of the US.

Manning's trial, which begins on 3 June, will be the highest-profile prosecution of the source of a leak of state secrets under the Obama administration. Since coming to office in 2009, Barack Obama has presided over more prosecutions of state leakers than all previous administrations combined, with six legal actions brought under the 1917 Espionage Act. The trial has been marked down for 12 weeks and could involve hundreds of witnesses. Four of those witnesses, it has already been agreed, will be presenting evidence secretly under a "light disguise", with the court moving to an undisclosed location for the duration.

The four include "John Doe", one of the US Navy Seals who raided Bin Laden's compound in Abbottabad, Pakistan and killed him on 2 May 2011.

In Tuesday's proceedings, Manning accepted through what is known as a "stipulation of fact" that the government had evidence that Bin Laden had taken a close personal interest in the material published by WikiLeaks. Manning has agreed not to contest the fact that when the Navy Seals left the compound they took with them several items of digital media that included a letter from Bin Laden to a member of al-Qaida, requesting that the member gather Department of Defense material posted to WikiLeaks.

The stipulation that Manning has accepted says that the digital items also contained a letter to Bin Laden from the same al-Qaida member to which the Afghanistan "war logs" – one of the most famous products of the WikiLeaks disclosures – were attached. Department of State information released by WikiLeaks was also among the Abbottabad discoveries.

The judge presiding over the court martial, Colonel Denise Lind, issued a ruling in which she outlined how classified information could be used during the trial. She said that within limits the prosecution could use classified documents to show that the material Manning transmitted to WikiLeaks could potentially be damaging to US interests.

In turn, the US government will have to prove beyond reasonable doubt that the soldier had "reason to believe" that the information he was leaking could be used to the injury of the US or the advantage of any foreign nation. The government would also have to show that the documents were "closely held" – in other words, that they were guarded as secret and not widely available to the American public.

During the course of the trial, the court will close to allow secret testimony to be heard from 24 specified witnesses. Lind ruled that in these cases examination would take place without the public and media present.

Lind made her ruling in the light of a dummy session that was held on 8 May in which a prosecution witness, Ambassador Donald Yamamoto, was quizzed in what was billed as a "dry run" for the trial. On the back of that, the judge found that alternative ways of dealing with classified information in front of the public – such as testifying electronically or using codenames – would not prevent the spillage of material that could be damaging to US national security.

Where the testimony related to classified information, Lind ruled, the court would be closed. A transcript of the secret proceedings, redacted to remove sensitive information, would then be released to the public.

"The over-riding interest in protecting national security over-rides the risk of miscarriage of justice," Lind concluded, adding that it also over-rode Manning's First Amendment rights.