A new study of the extremist Jemaah Islamiyah movement says the group may have been set back by recent arrests – but is far from stalling in its plans to carry out a holy war – or jihad – in the region. In fact, the report's author says she's has had to reassess the size of the organisation that was behind the Bali bombing and dozens of similar attacks across the region.

Presenter/Interviewer: Tim Palmer, Indonesia Correspondent

Speakers: Sidney Jones, of the International Crisis Group

Tim Palmer: The latest International Crisis Group report reaches conclusions that have come as a surprise to its author, Sidney Jones, the pre-eminent authority on JI in the region.

The group is not only bigger than she believed, but its members have coped with the arrest of figures like Hambali and Mukhlas by promoting men with similar skills and decentralising training and command.

Bomb making skills previously learnt by the old leadership in Afghanistan, then the Philippines, are now being passed on through small groups in Indonesia itself.

Sidney Jones: When I started this research I thought we were dealing with a few hundred, and now I think we're dealing with thousands. I think that in many ways they've got the capacity to keep going even with many of their top operatives behind bars.

Tim Palmer: Looking at some of the top operatives behind bars, people like Hambali, the key Bali bombers, and others caught subsequently in Sumatra, and a Semarang cell broken, there seems to be a suggestion if just a few of the key wanted men possibly Zulkarnain, Zulkifli, Dr Azahari can be rounded up that will have spoken the spine of the knowledge of weapons making in particular of JI. Is that the case?

Sidney Jones: I don't think it is the case, because in addition to the hundreds that went through Afghanistan training and hundreds more that went through Mindanao training, we see some people who've come back from those courses who have the capacity to train others.

In many ways, what they got in Afghanistan and the Philippines was a course in training the trainers, and we've seen actual evidence of one month courses taking place for example in south Sulawesi in how to make a bomb.

Tim Palmer: This is not technology that requires months with al-Qaeda?

Sidney Jones: That's right, you can do this in your own backyard with four, five other people and learn the basic techniques. And what that means in terms of the capacity do violence in Indonesia, or indeed elsewhere in the region is that you may have the top leadership pretty much under wraps, but you could still have just a wide swathe of people who are both capable and determined to make bombs even at a local level.