GUANTANAMO BAY NAVY BASE, Cuba -- The military has assigned an Army colonel to take over the upcoming war crimes trial of alleged Sept. 11 mastermind Khalid Sheik Mohammed, a sign that the Pentagon is plunging ahead with plans for military commissions of alleged 9/11 co-conspirators.

Army Col. Stephen R. Henley replaces Marine Col. Ralph Kohlmann, who at an earlier 9/11 hearing revealed he was retiring from active-duty service in April. He will join a legal clinic at Camp Lejeune, N.C., as a civil servant.

Henley has been a military judge for 10 years and has a law degree from George Washington University. As an Army judge, he presided at the courts martial of Maryland soldiers accused of abusing prisoners at Abu Ghraib, Iraq. As a commissions judge he is the only officer so far to exclude a confession on grounds it was derived from torture.

The American Civil Liberties Union derided the timing of the assignment: a day after President-elect Barack Obama restated his vow to close the prison camps here in a post-election interview on CBS' 60 Minutes.

ACLU Executive Director Anthony Romero called the timing ''highly suspect and disturbing'' and a bid "to sabotage President-elect Obama's plans by ramming through these cases . . . while the new administration is making plans to dismantle the military commission system.''

War court spokesman Joe DellaVedova said there was nothing sinister about the timing or the selection of Henley by Kohlmann to replace him.

''Retirements happen all the time in the military,'' said DellaVedova, a civilian who had been an Air Force public affairs major. He called the announcement, three weeks before the next 9/11 hearing at Guantánamo, ``an effort to establish some continuity for the accused.''

At issue is what, if anything, a future Obama administration would use in place of military commissions, the special post-9/11 war court the Bush administration created to prosecute accused terrorists as war criminals.

Obama has said that he wants terror suspects tried in criminal courts or perhaps in some instances by traditional military courts martial.

The ACLU, which has mounted a defense fund for those accused in death penalty cases at Guantánamo, wants Obama to close the commissions by executive order on Inauguration Day and switch cases that should be prosecuted to traditional courts.

The ACLU's ''John Adams Project'' funds seasoned civilian criminal defense attorneys working with Pentagon lawyers assigned to the five 9/11 suspects for whom the prosecution proposes military execution.

Mohammed and four others allegedly financed, orchestrated and trained the Sept. 11, 2001, hijackers who killed nearly 3,000 people in New York, Pennsylvania and the Pentagon.

The timing leaves Henley to decide some thorny pretrial issues, among them what evidence might be heard about the treatment of the five men across years of secret CIA interrogation before their arrival at Guantánamo in September 2006.

The spy agency has confirmed it waterboarded Mohammed to extract al Qaeda secrets.

Also still hanging is what to do about the mental health status co-conspirator Ramzi bin al Shibh, a Yemeni who is being prescribed psychotropic drugs at a secret detention facility here called Camp 7.

In pretrial hearings, the two judges have displayed starkly different styles.

Kohlmann is a sharp-tongued Marine who at the commission chambers has allowed the accused terrorists to deliver monologues but displayed little patience for attorneys.

On occasion he has cut off an attorney's effort to argue a point with, ''Which part of no do you not understand?'' Or, ``Sit down.''

Henley has shown more patience, particularly at the pretrial hearings of a young Afghan, Mohammed Jawad, in which he engaged in legal discussions with military defense attorneys.

He also has excluded Jawad's Kabul confessions from his upcoming January trial. In a war court first, Henley ruled that an accused was tortured -- notably through threats against his family -- while he was interrogated at an Afghan police station into confessing that he threw a grenade in December 2002 that maimed two U.S. soldiers and their Afghan interperter.

Henley's first 9/11 hearing is scheduled for Dec. 8, when the Pentagon has plans to bring down five family members of those killed on Sept. 11 to watch the proceedings.

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