Attorney General Eric Holder has taken a lot of heat for his decision to try the accused Sept. 11 plotters in a civilian court. But if the White House changes course and returns the suspects to military commissions, Holder may be in an even worse position, the Wall Street Journal reported Wednesday.

Attorney General Eric Holder (photo by Ryan J. Reilly).

According to DOJ officials, Holder’s decision to try Khalid Sheikh Mohammed and his four alleged co-conspirators in civil courts was predicated in part on President Barack Obama’s speech at the National Archives last year, the Journal said. “First, whenever feasible, we will try those who have violated American criminal laws in federal courts—courts provided for by the United States Constitution,” Obama said in May.

Justice Department officials admitted to the Journal that they failed to sufficiently reassure local residents after Holder’s announcement, but expressed frustration that the White House blocked Holder and others from publicly speaking out in defense of the decision.

According to the paper, Holder told friends he thought he had Obama’s support for the civilian trials. But White House Chief of Staff Rahm Emanuel opposed the idea, the Journal said.

According to the Journal, White House officials said they were now leaning toward a military trial for KSM and the alleged co-plotters as part of an effort to cut a deal with lawmakers on closing the detention facility at Guantanamo Bay.

Sen. Lindsey Graham (R-S.C.) is a key player in the deal and has said his support for closing Guantanamo is conditional on military trials for Mohammed and the others. However, there are still doubts about winning support from several Democrats, administration officials and congressional aides said.

The American Civil Liberties Union blasted the potential reversal in a full-page ad in the New York Times on Sunday. Anthony Romero, the ACLU’s executive director, told the Journal that a reversal would undermine the Justice Department’s reputation as non-partisan.

“Any reversal would clearly indicate that the decisions of the Justice Department are much more politicized than we were led to believe,” Romero said. “This Justice Department needs to show more incontrovertibly that it stands on its own two feet.”

In a full page ad in the Sunday New York Times, the American Civil Liberties Union appealed to President Barack Obama to keep the trial of the Sept. 11 plotters, including alleged mastermind Khalid Sheikh Mohammed, in civilian courts.

In November 2009, Attorney General Eric Holder announced that the Justice Department would try KSM in New York City near the site of the World Trade Center attacks. After initially expressing support for the trial, New York City business leaders and Mayor Michael Bloomberg changed course, complaining in January about the potential cost and disruption of a trial in Manhattan. Last week, The Washington Post reported that President Obama’s advisers are close to recommending that the DOJ return KSM to a military tribunal for prosecution.

In the ad, which features an image of Obama morphing into President George W. Bush, the ACLU calls on the president to support Holder’s original plan to try KSM and other Sept. 11, 2001, conspirators in civilian courts.

The ACLU has been critical of several of Obama’s national security and terrorism policies, saying his administration is beginning to have too many similarities to the Bush administration, such as a reliance on a “state secrets” privilege to keep information on some terrorism suspects out of court.

Anthony Romero, executive director of the ACLU, recently criticized the shift to military commissions, saying if such a change is made Obama would deal “a death blow to his own Justice Department.”

The full page ad the ACLU took out in the Sunday New York Times.

President Barack Obama’s advisers are “nearing a recommendation” that the self-proclaimed mastermind of the Sept. 11, 2001 terrorist attacks, Khalid Sheikh Mohammed, return to a military tribunal for prosecution, the Washington Post reports.

The alleged 9/11 mastermind in photographs released by the FBI in 2001. (Getty Images)

Eric Holder (photo by Ryan J. Reilly)

The White House had already overruled Attorney General Eric Holder’s decision, announced with fanfare in November, to try Mohammed in New York City, near the site of the demolished World Trade Center towers. That reversal came after New York City business leaders and Mayor Michael Bloomberg complained in January about the cost and disruption of a trial in Manhattan.

Bloomberg’s remarks set off a stampede among Democratic officials, who rushed to oppose a trial in Manhattan, prompting the administration to look for a new venue.

Then came hints that the administration would drop the whole idea of civilian trials for KSM, as Mohammed is known in government circles, and other Guantanamo Bay detainees. The White House was struggling to win support in Congress for closing Guantanamo Bay, after blowing a self-imposed one-year deadline for shuttering the military detention facility in Cuba. Civilian trials were an obstacle to winning that support.

ACLU's Anthony Romero

Civil liberty groups, already queasy about Obama administration policies that hewed in their view too closely to the George W. Bush administration, such as a reliance on a “state secrets” privilege to keep information on some terrorism suspects out of court, began bracing for the worst.

With today’s report that KSM isn’t likely to be tried in civilian court at all, Anthony Romero,executive director of the American Civil Liberties Union, doesn’t hold back.

“If President Obama reverses Holder’s decision to try the 9/11 defendants in criminal court and retreats to using the Bush military commissions, he deals a death blow to his own Justice Department, breaks a clear campaign promise to restore the rule of law and demonstrates that the promises to his constituents are all up for grabs,” Romero told the Post.

“The military commissions have not worked, they are doomed to failure, and Obama will invariably find himself running for office again while not achieving justice for the 9/11 attacks,” Romero said.