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Indonesia has killed or captured most of the militants responsible for the 2002 Bali bombings, but it now faces new threats from second-generation jihadists inspired by the 9/11 attacks.

Even before the strikes on New York and Washington on September 11, 2001, Southeast Asian militants were using the tactics of terror in their own war to create an Islamic caliphate across much of the region.

Groups such as Jemaah Islamiyah, which was founded by Indonesian exiles in Malaysia in the early 1990s, were already blamed for several attacks including bombings against churches and the Indonesian stock market in 2000.

But it was the spectacular "success" of 9/11 and the subsequent US invasion of Afghanistan that galvanised them to join the war against what Al-Qaeda leader Osama bin Laden called the "far enemy" - or Westerners.

The massive suicide bombings of tourist bars and restaurants on the Indonesian resort island of Bali on October 12, 2002, killed 202 people including 88 Australians.

But while jihadists celebrated, the blasts forced Indonesia, the United States and Australia to wake up to the terror threat in Southeast Asia, particularly Indonesia and the southern Philippines.

US and Australian advisers began pouring into Indonesia to help the democratically elected government, still finding its feet after the fall of the Suharto dictatorship in 1998, to confront JI and its affiliates.

But despite a string of successes in the years that followed as top militants were neutralised one by one, Indonesian National Anti-Terror Agency chief Ansyaad Mbai said that if anything, the danger has increased.

"The problem of terrorism is motivated by radical ideology, so the movement doesn't automatically end with the capture and death of key figures," he told AFP.

The Al-Qaeda-linked JI has "metamorphosized" into multiple new threats, he said.

"These small, autonomous groups aren't dependent on a top leader, they are only bound by ideology. They can move as small groups or as individuals, determine their own targets and execute plans on their own," Mbai said.

"They have high militancy levels due to their strong belief in the ideology, and they're very fanatical... The fact is that these groups are becoming stronger."

After the shock of Bali, the first breakthrough came with the arrest in 2003 of key Indonesian JI leader Hambali, an Al-Qaeda conduit accused among other things of plotting to blow up US airliners.

After another attack against Western tourists in Bali in 2005, JI bomb-maker Azahari Husin, a Malaysian, was killed by US-trained Indonesian anti-terror police at a hideout on Java island.

By this stage, analysts say, JI was feeling the pressure, and splits began to emerge between those who wanted more indiscriminate killing in the style of Al-Qaeda and others who argued too many Muslims were falling victim.

Another Malaysian, Noordin Mohammed Top, left JI to launch his own operations, including the last major terror attack in Indonesia - the 2009 suicide bombings of luxury hotels in Jakarta which killed seven people.

Some analysts saw the attack as Noordin's revenge for the November 9, 2008 execution by firing squad of Bali bombers Amrozi, Mukhlas and Imam Samudra. Two months after the hotel blasts he was killed in a shootout with police on Java.

Since then there have been more successes than failures for Indonesian counter-terror forces. A new cell dubbed Al-Qaeda in Aceh was discovered on Sumatra island last year, and its leaders were quickly killed or arrested.

Police killed another JI leader and Bali mastermind, Dulmatin, last year, while JI's main ideologue, radical cleric Abu Bakar Bashir, was jailed for 15 years on terrorism charges in June.

Pakistani police arrested the last alleged Bali mastermind still at large, Indonesian militant Umar Patek, earlier this year in the same town where Bin Laden was killed by US commandos. Patek is now awaiting trial in Indonesia.

Jakarta-based analyst Noor Huda Ismail, of the Institute for International Peacebuilding, said Indonesian militants had temporarily lowered their sights to target local police and officials in small-scale attacks.

"But this is only temporary - they are waiting for the right moment to attack foreigners again," he said, adding that the government had "a lot of homework" to do on issues such as the radicalisation of inmates in prisons.

In the Philippines, where Abu Sayyaf militants killed seven Marines on Jolo island only last month, security analyst Rodolfo Mendoza said the battle against Islamic militancy was as hot as ever.

"We have not realized the victory against the Abu Sayyaf and terrorism... They have active cells and existing alliances with other groups, like the JI," he said.

AFP