The government announced the decision in a letter Sunday to U.S. District Judge Lewis A. Kaplan, saying it would be ready to begin the trial against Ahmed Khalfan Ghailani on Tuesday.
In the letter, Assistant U.S. Attorney Michael Farbiarz noted that the government disagreed with Kaplan's decision and that it was something that would merit an appeal. But he said the government was prepared to prove its case without witness Hussein Abebe, and that other witnesses and victims had already traveled to New York for the trial.
"An appeal at this juncture would obviously cause a delay - a delay of uncertain, and perhaps significant, length," the letter said. "Weighing all of the circumstances, the government does not wish to delay the trial in order to take an appeal."
Ghailani has been accused by the government of being a bomb maker, document forger and aide to Osama bin Laden. He's charged with conspiring in the 1998 bombings of two U.S. embassies in Africa. The attacks killed 224 people, including a dozen Americans.
Ghailani has pleaded not guilty and has denied knowing that TNT and oxygen tanks he delivered would be used to make a bomb.
The judge said last week that Abebe could not take the stand in Ghailani's trial because investigators learned of his existence through coercive questioning of Ghailani at a secret CIA-run camp.
The decision came after a hearing a few weeks ago in which Abebe testified about his dealings with authorities.
"The court has not reached this conclusion lightly," Kaplan wrote in his decision. "It is acutely aware of the perilous nature of the world in which we live. But the Constitution is the rock upon which our nation rests. We must follow it not when it is convenient, but when fear and danger beckon in a different direction."
During that hearing, defense lawyer Peter Quijano tried to show that Abebe felt coerced to testify because he feared law enforcement, but Abebe insisted that was not so.
Another lawyer for Ghailani, Steve Zissou, said the government's decision not to appeal was "a significant victory for the Constitution. As we saw during his testimony, Mr. Abebe was hardly a credible witness."
There was little controversy when Ghailani was brought to New York for trial in 2009, but the subject of where to try Guantanamo Bay detainees became heated after Attorney General Eric Holder announced last November that the professed 9/11 mastermind Khalid Sheikh Mohammed and four others would be tried blocks from where the World Trade Center stood. Holder later said he was reconsidering the decision.