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Confirmation that President Barack Obama might back away from the plan came amid growing opposition from national and New York politicians, worried in part about the disruption a Manhattan trial would cause, and its projected billion-dollar price tag.
The Obama administration "was considering other options," an administration official said, speaking on condition of anonymity.
Another official said that "conversations have occurred within the administration to discuss contingency options should the possibility of a trial in Lower Manhattan be foreclosed upon by Congress or locally."
Several alternative sites have been aired, including towns outside New York city, a federal prison in Otisville and Stewart Air National Guard Base.
However each has its own logistical problems, meaning that a quick solution is unlikely.
The Obama administration says it is right to try Khalid Sheikh Mohammed, who claims he organized the September 11, 2001 attacks, and four Al-Qaeda co-accused, in southern Manhattan's federal courthouse.
The location is just blocks from where the World Trade Center once stood before hijacked airliners slammed into the Twin Towers. Nearly 3,000 people were killed there, at the Pentagon and in a field in Pennsylvania during the coordinated attacks of that day.
The trial is a major component of Obama's broader plan to close the military prison at Guantanamo Bay, Cuba, and end what he sees as widespread legal abuses under his predecessor, George W. Bush.
The idea has also provoked a political storm from Republicans and some 9/11 survivors and victims' families, who say terror suspects should not be protected by US laws and that trying Mohammed near Ground Zero is morally wrong.
More recently, pressure has grown from New York businesses and officials worried about disruption and security risks in the area close to Wall Street and Chinatown.
New York Mayor Michael Bloomberg, who initially welcomed the White House plan, abruptly reversed his stance this week, saying he would prefer a different location.
"It would be great if the federal government could find a site that didn't cost a billion dollars, which using downtown will," he said.
He was joined by other New York elected officials, including Senator Chuck Schumer, who said Thursday he was pressing the White House "to find suitable alternatives."
On Friday, Bloomberg repeated his disapproval. "It's going to be phenomenally expensive and it is very disruptive to people who live in the area," he told local radio.
"Some of the suggestions make sense, like a military base, because it's far from other people and you can provide security easily."
The most frequently touted alternative locations do not promise easy fixes.
The Stewart air base has no prison or courtroom, while the Otisville prison has no court. Bloomberg has dismissed suggestions of using Governor's Island, which is just off Manhattan and can only be reached by ferry.
Only the mayor of Newburgh, close to Stewart air base, appears to welcome the prospect of hosting the trial.
"I look on it almost as a tourist attraction. The international attention would put Newburgh on the map," he told the New York Post.
No trial date has yet been set and for now the five accused -- Sheikh Mohammed, Ramzi Binalshibh, Walid bin Attash, Ali Abdul Aziz Ali and Mustafa Ahmed al-Hawsawi-- remain in Guantanamo.
The row is the latest blow to Obama's agenda, just days after his Democratic Party lost a crucial Senate seat.
Obama is finding himself particularly vulnerable to Republican attacks on his handling of security.
Tensions rose further since the administration admitted widespread intelligence snafus leading up to an attempted Christmas Day bombing of a US airliner by a Nigerian allegedly working for Al-Qaeda.
The White House has yet to comment officially on switching trial locations.
After eight New York lawmakers wrote about their concerns to Attorney General Eric Holder on Thursday, a White House spokesman said Obama stood by the principle of giving terror suspects a civilian trial, rather than trying them in military tribunals.
Some lawmakers and Rudy Giuliani, who was mayor of New York at the time of the attacks, have urged the administration to prosecute the men before military courts that would afford fewer legal protections.
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