Roughly 85 per cent of Indonesia’s 240 million people profess Islam, making the country the world’s most populous Muslim-majority nation. Indonesian Islam is diverse, with virtually every variation of the faith represented, from mystical Sufism to politically radical fundamentalism, though there are very few shias.

Except for an extremist fringe, most Indonesian Muslims are moderate, and they tolerate each other well. They generally agree, however, that the government-persecuted Ahmadiyya sect, which claims to be “Islam,” is unacceptably nothing of the kind.

The sect’s refusal to give ground on this point is has made it a soft target for fundamentalist mobs and put the government of President Bambang Susilo Yudhoyono in a dilemma. If the president allows Ahmadiyya to exist in accordance with Indonesia’s constitutional guarantee of religious freedom, it will provoke more violence, and he may lose some much-needed Muslim political support in next year's election.

Ahmadiyya, founded in India in the late nineteenth century, was energetically seeking converts in Indonesia, then known as the Dutch East Indies, as long ago as the 1920s. The problem was (and is) that its founder, Hadrat Mirza Ghulam Ahmad, claimed to be a new, post-Mohammed prophet, as well as the Promised Messiah and Mahdi. This runs flatly contrary to the fundamental Muslim belief that Mohammed was the seal of the prophets, final as well as perfect.

The Islam-Ahmaddiya contretemps has something in common with the historic tension in the USA between Christianity and Mormonism, which was also founded by a break-away prophet. Mormons were persecuted in the US, often violently, until the church modified its doctrine to accommodate the Christian majority, most notably by outlawing polygamy. But Ahmadiyya has refused to question its founder’s prophethood or to drop its claim to be just as Islamic as anyone else.

Indonesia has got past the widespread communlal violence and terrorism which followed the fall of Suharto, epitomized by the Bali bombing of 2002, but militant radical groups such as the Islamic Defenders’ Front (FPI) are still eager to prove what vigilant Muslims they are, and Ahmadiyya, thanks to its obvious doctrinal deviation, makes a perfect target.

In 2005 the controversial, quasi-official Indonesian Council of Ulamas issued a non-binding fatwa (decree) reasserting that Ahmaddiyya is heretical, and this has been followed by sporadic mob violence against the sect’s followers and mosques ever since. The government has been unable to stop what is patently illegal violence. Recently the authorities offered Ahmadiyya a choice: it could stop claiming to be Muslim, in which case it would enjoy Indonesia’s constitutionally guaranteed freedom of religion, or it could close up shop.

Such a solution might have placated Muslim radicals, but Ahmadiyya, which has about 200,000 followers in the country, refused to renounce its Islamic identity or to go out of business. Instead it is appealing the government’s either-or decision. On 1 June, when supporters of religious rights, including prominent mainstream Muslim figures, staged a rally in Jakarta to support the sect, they too were attacked by a mob.

In some ways the Ahmadiyya case is a distraction from the more important competition between Islamic extremists and the moderate majority of Muslims, which the moderates seem to be gradually winning.

There has been no terrorist violence in Indonesia since 2005, and the country’s decentralized democracy is working well, with spirited elections at all levels frequently lost by incumbents. But Indonesians and foreigners alike are justifiably concerned about the continuing threat to pluralism and minority rights which the Ahmadiyya case demonstrates. Until the government is willing to uphold a basic freedom spelled out in its own constitution and crack down on mob violence, Indonesia will not get full moral credit for its undoubted democratic achievements.