Until Saturday night, there were grounds to hope that Indonesia’s popular, reforming President might have achieved a quiet breakthrough against the extremists bent on recasting much of South-East Asia as a theocratic state. Then three massive explosions on the Balinese south coast put such optimism in its place. In the world’s most populous Muslim country, despite President Yudhoyono’s admirable intentions and the unprecedented international support they have earned him, it is bombing season again.

The footsoldiers of Jemaah Islamiya, the Indonesian jihadist group with ties to al-Qaeda, have struck at around this time each year since 2002, when they killed 202 people in Bali’s nightclubs and restaurants. In 2003 they bombed a Marriott hotel in Jakarta. Last year they targeted the Australian Embassy there, killing 11 Indonesians but failing to penetrate the compound’s security cordon. This year they returned to the softest of soft targets: the beach.

The new wave of images of carnage is as shocking as the last, but to react with much surprise would be naive. Mr Yudhoyono has been in power less than a year. Jakarta’s control over the outer reaches of the Indonesian archipelago remains tenuous, and while only a tiny minority espouses the jihadism behind the bombings, its roots go deep. Though it did not emerge as a serious terrorist threat until the 1990s, Jemaah Islamiya traces its origins back three quarters of a century to the dream of an Indonesian Islamic state espoused by the Darul Islam group before independence from the Dutch.

The international business community in Jakarta, which exists behind metal detectors and concrete blast walls, may be resigned to the threat of violence. Mr Yudhoyono cannot afford to be. His clear popular mandate gives him an historic chance to tackle the causes and perpetrators of Indonesian terrorism without the paralysing fear of a grassroots backlash that prevented his predecessors from acting decisively. He should, specifically, stop equivocating on the threat from Jemaah Islamiya, whose very existence he has been known to question. He must also demand greater efforts to bring its key strategists to justice.

Indonesia’s two most-wanted men, including a bombmaker with a doctorate from Reading University, remain at large despite a presidential pledge last year to apprehend them within the first 100 days of the new administration. Jemaah Islamiya’s spiritual leader, Abu Bakar Bashir, has meanwhile been treated with startling leniency despite actively encouraging terrorist recruits to “kill Americans”.

Jakarta’s challenge is to rein in known extremists without making martyrs of them or radicalising their followers further. To this end, it must also push through reforms of its notorious security apparatus, whose past brutality has helped to foster jihadism and separatism alike.

For all its international ties, Indonesia’s terrorist scourge is largely home-grown. Jakarta deserves the wider world’s support, but the task of neutralising this threat is, ultimately, its own.