In a sign of disunity at the Pentagon over the coming Sept. 11 trial, a senior Defense Department official on Friday refused to scratch a conspiracy charge from the death penalty case, a move sought by the prosecution to make any future conviction less vulnerable to civilian appeal.

Army Brig. Gen. Mark Martins, the chief war crimes prosecutor, disclosed on Jan. 9 that he decided not to pursue the conspiracy charge in the Pentagon’s highest profile Guantánamo case to “ensure the prosecution proceeds undeterred by legal challenge.”

But retired Navy Vice Adm. Bruce MacDonald, a lawyer who has oversight of the war court, refused to remove the charge in a decision announced on Friday afternoon, said Army Lt. Col. Todd Breasseale, a Pentagon spokesman.

The development is the latest tug-of-war over how to put on trial alleged Sept. 11 mastermind Khalid Sheik Mohammed, the former CIA captive who was waterboarded 183 times, and four other alleged trainers and financiers of the 19 men who hijacked four planes on Sept. 11, 2001, killing nearly 3,000 people.

Attorney General Eric Holder wanted the men tried in a traditional federal court, before a civilian judge and jury in New York City. Congress blocked the trial. So Holder turned the case over to the Pentagon.

Now the civilian courts are looking at the authority of the tribunals created by President George W. Bush and reformed by President Barack Obama. One question is whether conspiracy is a war crime. It’s not in international courts, and the prosecutor has said a civilian court might overturn a conspiracy conviction. He wants to use the other more well-established war crimes charges — murder, terrorism and attacking civilians.

That threat of a conviction being overturned on appeal is real.

A civilian court in October overturned the 2007 Guantánamo conviction of Osama bin Laden’s driver, Salim Hamdan. His military jury found him guilty of providing material support for terror, a war crime created in 2006, for crimes that occurred before his capture, in 2001. Congress also created conspiracy as a war crime in 2006 — five years after the Sept. 11 attacks.

MacDonald “noted that dismissal at this time would be premature,” said Breasseale, “as the viability of conspiracy as a chargeable offense in trials by military commission is still pending appellate review.”

But Martins may have already anticipated Friday’s setback to his ambition of more narrowly tailoring the Sept. 11 trial.

On Wednesday, he filed a sealed motion entitled “Government Motion to Make Minor Changes to the Charge Sheet” asking the war court judge, Army Col. James Pohl, to use his authority to scratch the conspiracy charge. It was still under seal Friday, but attorney Jay Connell, defending alleged 9/11 conspirator Ammar al Baluchi, said the motion includes a copy of the charge sheet with Charge No. 1, Conspiracy, scratched out with a trademark military prosecutor’s “Z.”

In the motion, prosecutors propose to retain a 167-item narrative that describes the alleged “conspiracy” — but as a free-floating introduction of sorts that goes on for 17 pages before it reaches the first charge brought to trial, Attacking Civilians. Murder and terrorism follow.

The flurry of filings comes as lawyers prepare for Jan. 28-31 pre-trial hearings in the case.