The Bali attacks killed 202 people
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A new generation of militants is being groomed by South East Asia's Jemaah Islamiah group to carry out more Bali-style bombings, Singapore has warned.
Home Affairs Minister Wong Kan Seng said JI was rebuilding after recent arrests, training leaders in religious schools in Indonesia and Pakistan.
"Troubled times are going to last for a long time," he said.
JI, which some governments link to al-Qaeda, has been blamed for the Bali attack and a hotel bombing in Jakarta.
"As an organisation it is only disrupted, it is by no means eliminated," he said.
Mr Wong highlighted the September arrests of 19 suspected JI members studying in a religious school - known as pesantren or madrassas - in Pakistan.
"Trained in both religious and military and terrorist skills, these young men were being groomed to be the next generation of leaders in the JI," he said.
Mr Wong said the group included sons of Malaysian, Indonesian and Singaporean JI members, and was set up by the son of Abu Bakar Ba'asyir, the group's alleged spiritual leader.
An attack on Jakarta's Marriott Hotel left 12 dead
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"In Indonesia, the next generation of JI soldiers are also being groomed in JI-controlled religious schools," he said.
But Marty Natalegawa, spokesman for the Indonesian foreign ministry, said Singapore was "stating the obvious" about the continuing threat in the region.
"The JI network is not the monopoly of one or two countries," he said. "What is more important is identifying what steps should be taken to address it."
Mr Natalegawa said Indonesia was doing that, and it had carried out a number of successful operations against militant groups.
"But we don't have the mechanisms which some of our neighbours have, where they simply arrest people without due process," he added.
"We have to act in a manner which is in accord with our observing of civil liberties."
Vulnerable
Dr David Wright-Neville, of the Global Terrorism Project at Monash University, Melbourne, said the comments from Singapore were in line with previous warnings.
"They don't think anyone else takes JI seriously enough, and their position in the region makes them all the more vulnerable," he said.
"So they tend to always put a fairly pessimistic spin on things to worry their neighbours' neighbours, particularly Australia and America."
Dr Wright-Neville agreed that JI was still a threat, with a number of senior members still at large.
"I also think the group can replenish itself, although it takes time to rebuild all the skills."
Hambali was arrested in August
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A number of JI's leaders have been arrested recently, including the group's alleged head of logistics Hambali.
He was arrested in Thailand in August and is currently in US custody at an undisclosed location.
The man now leading JI's military operations has been named by some security analysts as Zulkarnaen, whose real name is Aris Sumarsono.
Dr Wright-Neville said Zulkarnaen was previously in charge of the illegal finance networks that funded JI.
"He has moved up the hierarchy, " he said. "He is bright and dangerous. He doesn't have the operational nous that Hambali had, but he is clever and capable of learning."