Radical Indonesian cleric Abu Bakar Bashir, a leader of the outlawed Southeast Asian militant network Jemaah Islamiah, arrives for his trial at the South Jakarta court in 2011.

Radical Indonesian cleric Abu Bakar Bashir, a leader of the outlawed Southeast Asian militant network Jemaah Islamiah, arrives for his trial at the South Jakarta court in 2011. Photo: Reuters

Indonesia still faces significant terrorism threats despite the dismantling of major Jihadist networks after the Bali bombings, a top expert says.

And the expert, Solahudin, has also said that mass data gathering by authorities such as the controversial US monitoring programs are likely helping combat the scourge because the internet is a key tool for Indonesian Jihadists.

Solahudin, who like many Indonesians goes by one name only, said that like many parts of the world, his country had broken up major terrorism networks but still faced a fragmented threat with many self-motivated extremists.

While attacks and threats were generally on a smaller scale compared with past years, they were more numerous, with 75 cases - either attacks, plots or threats - in the past three years.

"This diminished lethality does not mean we should be sanguine about terrorism in Indonesia," he says.

Documents leaked by former US surveillance analyst Edward Snowden revealed that Australia was among the countries helping with the US system X-Keyscore, which enables monitoring of "nearly everything a typical user does on the internet".

This allowed Australian intelligence officials to internet and telecommunications traffic across the Asia-Pacific region, including Indonesia, Fairfax Media has reported.

Solahudin, the author of a newly translated book The Roots of Terrorism in Indonesia, said such methods could help fight terrorism in his country.

"They would be very useful to combat terrorism," he said. "If you want to learn about bomb-making, weapons, even poison-making for assassinations, it's all there on the internet.

"People learn their ideology on the internet but also the tools and tactics."

He said more research into the underlying causes of self radicalisation was needed to combat terrorism in its new form.

"The problem with the Indonesian government is that they have no idea what are the root causes of terrorism in Indonesia."

Indonesian police had been effective in breaking up organisations such as Jema'ah Islamiyah, which was behind the 2002 Bali bombing that killed 202 people including 88 Australians, Solahudin said.

But Indonesia had been less successful in fighting the root ideology that inspired Islamic extremists, with many Indonesians refusing even to see a connection between religious extremism and terrorism.

Today's attacks were smaller in scale and usually targeted the Indonesian government or local officials, rather than foreigners or Western targets.