15/10/2012 06:19 BST | Updated 13/12/2012 05:12 GMT

As a friend, Britain Should Warn Indonesia That Its Pluralism Is in Peril

Indonesia's president Susilo Bambang Yudhoyono arrives in London at the end of this month, for a three-day state visit. It follows David Cameron's visit to Indonesia earlier this year, and signals a desire by both countries to strengthen their relationship.

There is much to celebrate and encourage in Indonesia. The world's largest Muslim-majority nation, an extraordinary archipelago of over 17,000 islands with a population of 242 million, has made a remarkable transition from authoritarianism to democracy over the past decade. The strand of Islam practised by the majority of Indonesians is very moderate, and the country has a great tradition of religious freedom and harmony. Indeed, although it has the world's largest Muslim population, it is not an Islamic state - its ideology, the 'Pancasila', enshrines religious pluralism.

It is right to invite President Yudhoyono to Britain, it is right to seek to deepen our friendship, and it is right to applaud Indonesia's achievements. But in a spirit of friendship, David Cameron and the British Government should not shy away from addressing the challenges as well as lauding the accomplishments. For there are two major issues which threaten Indonesia's status as a model of religious pluralism in the Islamic world and undermine its reputation for human rights and democracy: the rise of Islamist extremism, and the Indonesian military's abuses in West Papua.

Over the past decade, Islamism has reared its ugly head in Indonesia, and turned a previously pluralistic nation into an increasingly intolerant one. Islamists are still believed to be numerically in a minority, although their number is growing, but they appear to be gaining increasing influence. Religious minorities, particularly Christians, as well as Shi'a and Ahmadi Muslims, are facing growing violence, intimidation, restriction and discrimination. An atheist has been jailed because he does not believe in God. Muslims who speak up for pluralism, and secular voices, are increasingly threatened as well.

Earlier this year, Lady Gaga's concert in Indonesia was cancelled after Islamist groups threatened violence. Radicals attacked a lecture by liberal Canadian Muslim Irshad Manji. In Aceh, at least 17 churches were forced to close. In West Java, a growing number of churches have been closed, even though they have all the correct legal approvals. In two cases, the courts have ruled that the churches should be allowed to open, but the local Mayor, under pressure from radicals, continues to refuse. Both churches, not far from Jakarta, hold their Sunday services in the street outside. I have visited them, and found myself among a congregation surrounded by an angry Islamist mob shouting "Christians get out, kill the Christians" and "anyone not wearing a jilbab, hunt them down". In the case of GKI Yasmin Church in Bogor, the Mayor is supporting the mob in defiance of the Supreme Court, which ruled that the church should open. This is no longer just a religious freedom issue, it is a rule of law issue.

Last year I met victims of one of the worst outbreaks of violence, an attack on Ahmadi Muslims in Cikeusik on 6 February, 2011 which left three people dead. One man described how he was stripped naked, beaten to a pulp, a machete held at his throat with a threat to cut off his penis. He was dragged through the village and dumped in a truck like a corpse. Another fled into a fast-flowing river, pursued by attackers throwing rocks and shouting "kill, kill, kill." He hid in a bush, dripping wet and extremely cold, for four hours. A third suffered a broken jaw, while a fourth, pursued by men armed with sickles, machetes and spears, was detained by the police for three days, treated as a suspect not a victim. Of the 1,500-strong mob which attacked 21 Ahmadis, only three men were arrested and prosecuted. Their sentences were between three and six months.

In May, I met a pastor, Reverend Luspida, who was beaten while one of her congregation was knifed. She told me: "We have no religious freedom here anymore. We need to give a message to the President. He cannot say the situation is good here. We need to remind him our situation is very critical, and he should do something for the future of Indonesia. Support from outside is very important to pressure the President."

The long-running conflict in West Papua is the other major concern. Ever since it invaded West Papua half a century ago, the Indonesian military has been accused of horrific human rights violations: killings, rape, torture. This summer, one of the leaders of the Papuan resistance, Mako Tabuni, was killed. Several Papuan dissidents are in jail, including Filep Karma, whose only crime was to raise the 'Morning Star' flag, the symbol of independence. He was sentenced to 15 years.

On both these issues, there are voices of moderation working to find a solution. Muslim counter-extremism groups like the Wahid Institute and the Maarif Institute are providing a voice for pluralism. The Papua Peace Network, led by Father Neles Tebay from Papua and Dr Muridan Widjojo from the Indonesian Institute of Sciences (LIPI), advocate dialogue and have set out proposals in the Papua Road Map. President Yudhoyono, or SBY as he is known, should be encouraged to engage more actively with these actors.

In 2014, Indonesia will elect a new President. In his remaining two years in office, SBY has a chance to tackle these issues. The majority of Indonesian Muslims have no time for the radicals, but are afraid to stand up against them. If the President leads the way, however, he will have the majority of the country behind him. He should have the courage to uphold the rule of law, sack local Mayors who defy court orders, revise the blasphemy laws which are so widely abused, repeal anti-Ahmadiyyah decrees, protect religious groups' right to worship, ensure that perpetrators of violence are brought to justice and work with groups like the Wahid Institute to counter radical teachings. In West Papua, he should release all political prisoners, reduce the military's presence and initiate a meaningful dialogue process between his government and the Papuan people.

SBY is surely beginning to think of his legacy. Will he be remembered as the President who curbed extremism and enhanced human rights, protecting Indonesia's reputation for pluralism and strengthening its democratisation? Or will he be the President who allowed the Islamists to tear up the 'Pancasila' and the military to perpetuate their reign of terror in West Papua, thereby destroying Indonesia's remarkable achievements of the past decade? He has a choice, and as a friend of Indonesia, Britain should leave him in no doubt as to what he needs to do. His reputation, and his country's future, are at stake.