Greg Barton – Three years after the horror of the first Bali bombing and four years after the shock of the September 11 attacks, most Australians are mystified about why doubts about Jemaah Islamiah persist in Indonesia.

The recent comments, for example, of former president Abdurrahman Wahid suggesting that the Indonesian military somehow may have been involved in the attack on Bali's Sari Club on October 12, 2002, strike us as truly incredible.

To Australians, Indonesian scepticism about terrorism is hard to understand. After all, Indonesians and Indonesia have been, by far, the biggest victims of jihadi terrorism in the region. In fact, the extent of Indonesian suffering is much greater than commonly realised in Australia.

As many as 10,000 Indonesians have died in sectarian violence in eastern Indonesia since 2000. The communal violence in Maluku and Sulawesi did spring from organic causes but was so exacerbated by the presence of external Islamist militia such as Laskar Jihad that it is fair to say their intervention cost the lives of thousands.

It is tempting for Australians to simply dismiss the doubts and anxieties of Muslims in Indonesia and elsewhere about terrorism as evidence of delusion and denial. But to do that would be a grave mistake, for such fears, however ill-founded, often point to deep problems of communication and credibility on our part. It is time for us to stop viewing the problem of jihadi terrorism only through Western eyes and to attempt to see things from a Muslim point of view.

In our rush to fight terrorism we have underestimated the importance of perceptions and paid too little attention to how Muslim society understands what we do. The clumsy rhetoric of the war on terror has tended to undermine Western credibility in the Muslim world. In fact, the West has generally made a hash of communicating to the Muslim world while apologists for terrorism, such as Indonesia's Abu Bakar Bashir and his Indonesian Mujahidin Council, have given a series of virtuoso performances in public relations.

While Australian leaders and observers have tended to ignore or misunderstand Indonesian anxieties, Bashir and his colleagues have masterfully exploited the confusion of the Indonesian public about what JI is and what it is capable of doing, successfully sowing seeds of doubt. Some Indonesian politicians, it is true, have cynically exploited these circumstances for their own narrow interests. Wahid, however, is a different case. There can be no doubting his deep concern for Indonesia and his affection for Australia, and so we should not imagine that he is talking out of malice.

But neither can it be denied, as Sally Neighbour wrote in The Australian yesterday, that he is "famously eccentric". If his comments were merely the product of eccentricity, or worse, then they could be dismissed easily, but it is difficult to see that this is the case.

That Wahid has spent his life promoting tolerance and struggling against sectarianism, including Islamist extremism, is good reason for us to consider what he is saying: this is not a man who has any desire to downplay jihadi terrorism.

Indeed, he wrote an opinion piece published in last Friday's The Washington Post condemning the recent Bali suicide bombers, saying: "Once again the cult of death has proved its ability to recruit misguided fanatics and incite them to violate Islam's most sacred teachings in the very name of God." The worrying thing is that the kind of dark fears of military involvement that Wahid expressed are not uncommon and probably represent mainstream sentiment in Indonesia.

There is no evidence that the Indonesian military or police (they were separated in 1999) had any involvement at all in the October 12, 2002, bombings or that they have in any way supported JI. But there is considerable evidence, as Neighbour points out, of Indonesian military support for Islamist militia such as Laskar Jihad, initially given, in part, with the intention of discrediting the Wahid government.

We need to understand that after decades of repression and innumerable military dirty tricks, some of which continue, it is difficult for Indonesians at any level of society to believe that JI operates entirely by itself.

The situation today would be much worse were it not for the remarkably successful joint police investigations after the 2002 Bali bombings that led to hundreds of arrests, making possible transparent court trials and producing a great volume of credible evidence about JI.

Australia and Indonesia have worked well together. But the fact doubt about JI still runs deep in Indonesian society reminds us that the struggle against terrorism is also a struggle for hearts and minds, and that we need to lift our game.

[Greg Barton is associate professor in politics at Deakin University in Melbourne. He is author of Indonesia's Struggle: Jemaah Islamiyah and the Soul of Islam (UNSW Press, 2004) and Abdurrahman Wahid: Muslim Democrat, Indonesian President (UNSW Press, 2002).]