The detention facility in Bagram was administered by the US
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South East Asian officials have voiced concern at the escape of a suspected regional militant leader from US military custody in Afghanistan.
US prosecutors admitted on Tuesday that Omar al-Faruq was one of four detainees to escape from the Bagram base in July, all of whom are still on the run.
Indonesia's top anti-terrorism chief said his escape "increases the threat of terrorism".
Al-Faruq was seen as one of Osama bin Laden's key lieutenants in Asia.
Although the July escape was widely reported at the time, al-Faruq was only identified by an alias.
His identity came to light at the trial of a US soldier accused of abusing Bagram detainees, in which al-Faruq was due to testify.
A lawyer defending the soldier at Fort Bliss in Texas asked where al-Faruq was, and a prosecutor admitted he had escaped and had not yet been found.
'Dangerous'
Born in Kuwait to Iraqi parents, al-Faruq is thought to have been a link between al-Qaeda and the regional militant network Jemaah Islamiah (JI), which has been blamed for the Bali bombings and other attacks.
He is believed to have spent time training militants in the southern Philippine island of Mindanao, before moving to Indonesia for several years and allegedly setting up terrorist training camps.
He was arrested by the Indonesian authorities in June 2002, and was turned over to the United States, eventually ending up at Bagram.
It is not clear how he managed to escape from the heavily fortified detention facility, but US military spokesman Lt Col Jerry O'Hara issued a statement saying there were "shortcomings identified in the physical security of the facility that have [now] been corrected".
When asked about al-Faruq's escape on Tuesday, the Indonesian authorities had harsh words to say about the potential ramifications.
"This man is dangerous, and his escape increases the threat of terrorism in Indonesia," the country's top anti-terrorism chief, Maj Gen Ansyaad Mbai, told the Associated Press.
"We need to co-ordinate security here as soon as possible to anticipate his return," Mr Mbai said, adding that al-Faruq's wife and children still lived in Indonesia.
He also said he had not known about al-Faruq's escape, insisting the US authorities should have informed him.
Even al-Faruq's 27-year-old wife, Mira Agustina, said Washington had never told her about her husband's arrest or escape.
"He's vanished, I don't think he's going to reappear," she told the Associated Press.
Observers say the news is likely to add to Indonesia's frustrations with the US. The authorities in Jakarta are getting increasingly annoyed that they have not been given access to Hambali, another key militant suspect who was arrested in Thailand in 2003.
Hambali is being held in US custody at an undisclosed location.