The announcement came a month after lieutenant colonel Darrel Vandeveld, the former prosecutor for the five suspects, resigned after criticising his own office for withholding evidence helpful to the defence of another detainee.
Six military prosecutors have quit the Guantanamo court in the last four years.
Some have said that the US government sought to use evidence obtained through torture while one alleged the trials were tainted by political interference.
'False confessions'
Anthony Romero, the executive director of the American Civil Liberties Union, said: "The implosion of these five prosecutions painfully underscores how the Bush administration's torture and detention policies have failed to render justice in any sense of the word."
Noor Uthman Muhammed, Binyam Mohamed, Sufyiam Barhoumi, Ghassan Abdullah al Sharbi, and Jabran Said Bin al Qahtani had been charged with conspiracy and "providing material support for terrorism".
Binyam Mohamed, an Ethiopian-born British resident, had been accused of training and plotting "dirty bomb" attacks on targets in the US with Jose Padilla, a Chicago gang member once also accused of plotting a radioactive bomb attack.
Mohamed has said repeatedly that he is innocent and gave false confessions while being tortured in a Moroccan prison.
He had been transferred there extrajudicially after being captured in Pakistan and held for 18 months before being sent to Guantanamo.
'Cut and beaten'
Mohamed said he told interrogators what he believed they wanted to hear after he had been beaten, strung up by his arms and cut on his penis and chest with scalpels.
Susan Crawford, appointed by the Pentagon to oversee the tribunals, upheld charges on Tuesday against Mohammed Hashim, an Afghan detainee, of supporting terrorism and spying on US troops in Afghanistan.
Robert Gates, the US defence secretary later said the detention facility will not close before the Bush administration leaves office in January.
"This is an issue that'll have to be addressed early on by a new administration," he said.
The Pentagon also announced that it will allow victims of alleged terrorist attacks and their relatives to attend trials at Guantanamo.