A US prosecutor has asked the judge in the 9/11 military tribunal in Guantánamo Bay for more time to look into whether an FBI investigation will affect the stalled war crimes trial.

The assistant US attorney Fernando Campoamor Sanchez says he confirmed the FBI began a preliminary criminal investigation involving classified information, but argues he needs 30 days to respond to a defense request to abate proceedings against five Guantánamo prisoners charged with orchestrating the attack on 11 September 2001.

On 17 April the tribunal was adjourned until June, derailed by an attempt by the FBI to turn a defense team expert on classified materials into an informant. When the adjournment was decided the army judge in the case, Colonel James Pohl, said he was considering appointing independent lawyers for defendants Khalid Sheikh Mohammed and Ramzi bin al-Shibh to advise them of possible conflicts between their defense teams’ ability to represent them and the lawyers’ interest in defending themselves against an apparent FBI investigation.

The defense told the court last week that it understood the FBI was seeking information on how an unclassified manifesto penned by Mohammed in his Guantánamo cell made its way to the Huffington Post and the UK’s Channel Four. Pohl on Thursday ordered independent counsel for two detainees as an interim measure before establishing the full extent of the FBI penetration.

But on Monday Campoamor-Sanchez, the new US justice department special counsel brought into the prosecution to address the FBI allegation, declared that the “FBI preliminary investigation” of the defense teams did not concern the release of Mohammed’s manifesto, titled Invitation to Happiness.

“The FBI preliminary investigation does not pertain to the disclosure of Mr Mohammed’s written communications,” Campoamor-Sanchez told the tribunal in a late Monday filing.

The justice department lawyer did not address what actually compelled two FBI agents to approach at home on 6 April an unnamed classification specialist advising the defense teams. Campoamor-Sanchez said he would leave the wellspring of the FBI inquiry for a classified filing.

“[D]isclosure beyond the commission would jeopardize an ongoing FBI criminal investigation that involves, at least in part, classified information and a need to avoid potential serious harm,” Campoamor-Sanchez told the tribunal.

Campoamor-Sanchez requested another 30 days from Pohl to provide “an additional factual submission regarding the FBI Preliminary Investigation”. He also told Pohl that the rest of the prosecution was insulated from the FBI preliminary investigation.

For a week the unequivocal position of the prosecution has been that it knew nothing about why two FBI agents on 6 April approached an unnamed classification specialist advising lawyers for the 9/11 co-defendent Ramzi bin al-Shibh.

The defense told the court on Wednesday that it wished to talk to four FBI officials, including the chief of staff to the deputy director, who is detailed to the 9/11 tribunal prosecution team.

In his filing Campoamor-Sanchez intimated to Pohl that the defense teams might not face the conflict of interest they fear, but he did not provide information about the actual circumstances behind the FBI’s 6 April action.

The tribunal will not meet again until June. Even before the FBI spying allegations it was already inundated with pretrial motions that have pushed back the beginning of the trial phase of the military commission indefinitely.