The expulsion from Indonesia of the American terrorism expert Sidney Jones can only undermine the democratic credentials of the Megawati Government. Ms Jones, head of the Jakarta office of the Brussels-based International Crisis Group (ICG), is widely acknowledged as the world's top authority on the Indonesian-based Jemaah Islamiah (JI) Islamic terrorist network. Her departure at the weekend, however, probably says more about national pride and politics than Jakarta's stance on Islamic extremism.

Two months before the Bali bombings of 2002 Ms Jones published a detailed report describing the extent of the JI terrorist network in South-East Asia. Last year, her latest report concluded that JI was far from destroyed, despite the arrests of more than 200 of its senior members in Indonesia, Malaysia and Singapore. A new generation of jihadists, it said, was in the making in Islamic boarding schools across Indonesia.

Yet, it was not this blunt challenge to the Indonesia's anti-terrorism effort that seems to have so offended. Indonesia has consistently co-operated with Western security agencies, including the Australian Federal Police, since the Bali bombings. There is certainly popular resentment among Indonesia's majority moderate Muslims over Western stereotypes that associate Islam with terrorism. However, it is the ICG's scathing reports on the Indonesian military's operations against separatist forces in Aceh and Papua that are believed to have provoked Jakarta's ire.

International condemnation of the Indonesian military over the carnage in East Timor in 1999 – and the loss of the former Indonesian-occupied territory – was considered deeply humiliating in Indonesia. Many politicians, including President Megawati Soekarnoputri, have since insisted that national unity and pride depend on preventing a similar splintering in Aceh and Papua. As a fluent Bahasa Indonesia speaker Ms Jones – unlike many other foreign experts – was able regularly to bring ICG's frank views on these conflicts, and other politically sensitive issues such as corruption, into the domestic media.

A rumoured hit list of other individuals and organisations that threaten security before next month's presidential elections has, understandably, raised fears of a return to the repression that marked the authoritarian Soeharto era.

But unless such a crackdown is implemented it seems far more likely that Ms Jones's case is an exception to Indonesia's expanding freedom of speech – and a temporary one at that. Once the presidential campaign dust has settled it must be hoped Ms Jones will be allowed to return.