The defence teams for the accused 9/11 perpetrators have formally requested testimony from four officials from the Federal Bureau of Investigation, one of whom is a senior official, deepening a conflict that began with revelations that the FBI attempted to insert an informant into their ranks.

Defence lawyers said late on Wednesday that they had formally requested testimony from the two agents that approached a classification specialist assigned to the defence team, as well as an FBI special agent assigned to the 9/11 prosecution team.

But the defence also wants testimony from a senior FBI official detailed to the prosecution: Joanna Baltes, the chief of staff for the deputy FBI director, Mark Giuliano.

Baltes is not currently at Guantánamo. In court on Tuesday, defence lawyers openly speculated, without providing evidence, that she might have played a role in the FBI's unexpected involvement in an apparent inquiry seeking the source of a media leak – an unclassified manifesto written by accused 9/11 architect Khalid Shaikh Mohammed.

"There's a real question about whether there's a dual role [Baltes plays]," said Walter Ruiz, a lawyer for 9/11 co-defendant Mustafa Ahmed al-Hasawi.

"If there's a dual role, there's a huge question about a potential conflict of interest."

The move to call Baltes to testify comes with several unknowns. Chief among them is if the military commissions have the power to compel her to testify. Army Colonel James Pohl, the judge in the 9/11 tribunal, appeared unsure on Tuesday if he possessed that authority.

The FBI did not immediately respond to a request for comment about its willingness to allow Baltes or the three FBI agents to give testimony in the case.

Additionally, the military commission prosecution team is adding a Justice Department lawyer as a "special trial counsel" assigned to address any aspects of the FBI inquiry issue involving the prosecution. The lawyer, whose name was not immediately released, will not play any direct role in the 9/11 trial.

The defence lawyers said this week that their possible investigation as part of a leak inquiry potentially places them in a conflict of interest, pitting their need to defend themselves against their obligations to defend their clients. The prosecution has rejected that contention as premature.

Now the defence appears to be pointing to potential conflicts within the prosecution. Two sources said the FBI special agent assigned to the prosecution, Jim Fitzgerald, was the one who received the Mohammed document on 20 December from Brigadier General Mark Martins, the chief military commissions prosecutor who has prioritised making the commissions domestically and internationally respectable.

But the process has been called into question by the fact of the apparent FBI inquiry. On 6 April, two FBI agents approached a classification specialist at his home after church and got him to sign documents that indicated an ongoing informant role.

The existence of an ongoing inquiry into the defence, its basis, and the extent of the defence's penetration has now crowded out proceedings in the pretrial stage of the 9/11 case, further delaying the actual trial, more than 12 years after the terrorist attacks.

Several family members of the victims who had travelled to Guantánamo to attend the pretrial hearings expressed anger on Wednesday with the FBI and the Obama administration for potentially jeopardising the military trial outright.

It was unclear to attorneys late on Wednesday whether Pohl will hold a court hearing on Thursday morning.