Bahrain: The divided kingdom

Brutal crackdowns on Bahraini protesters have revealed a bloody rift between the country's Sunni rulers and the Shia majority. Sectarian violence could tear the nation apart – as it has done elsewhere, warns Patrick Cockburn

When two tribes go to war: anti-government protesters in Manama, Bahrain earlier this year

Is there a fatal connection between the initial letter "B" and places torn apart by struggles for power between different religious communities? I started as a journalist in Belfast in the early 1970s when the city was convulsed by sectarian warfare between Catholics and Protestants. In later years, I moved to Beirut to cover the many-sided civil war, at the heart of which was the conflict between Muslims and Maronites. After 2003, I spent long months in Baghdad, writing about the fighting between Shia and Sunni which culminated in the slaughter of 2006-7.

Even so, it is surprising to find Bahrain added to the list of places polarised and traumatised by sectarian differences, in this case between Shia and Sunni. The confrontation between the ruling Sunni minority led by the al-Khalifa royal family and the Shia majority is not entirely new. There have been crises in relations between the two in the past. But the ferocity and cruelty of what has transpired on this small island in the Gulf over the last five months has shocked and surprised its 1.2 million people, half of whom are Arabs.

Among those puzzled is Cherif Bassiouni, the highly distinguished Egyptian-American legal scholar, who has been asked by King Hamad bin Isa al-Khalifa to lead an inquiry into the events which followed the start of the Arab Awakening on 14 February. Compared to Iraq or Libya, Bassiouni notes that the casualties were light – about 33 dead – "but this relatively small number has had a traumatic effect on society". He describes the two sides as producing wholly different accounts of what happened. He says "it is like a murder scene where you have the dead body, but nobody can agree if the bullet came from the right or the left".

He is convinced he has the backing of the King and the Crown Prince for an inquiry which will be somewhere between a fact-finding investigation and a truth commission. He suspects that in order to reverse sectarian polarisation, a purge of the security forces may be needed as well as a government-backed programme for reconciliation.

Many Shia believe that the King will be unable or unwilling to deliver on his commitments to Bassiouni. Alaa Shehabi, the wife of a jailed Shia businessman, says: "It is a big problem if the King didn't know what was happening, and a bigger problem if he did know and is feigning ignorance." Many Sunni, for their part, object to concessions to what they see as an evil Iranian-orchestrated conspiracy.

One does not have to go far in Bahrain to find out why the Shia are so angry. In Graham Greene's Our Man in Havana, his fictional Cuban police chief Captain Segura distinguishes between two classes of people, the torturable and the untorturable. It is not a distinction that has made much impression on the Bahraini security forces, going by the wholesale repression that began on 15 March, which followed the arrival of a Saudi-led military contingent. Protesters in Pearl Square were beaten and the 300-foot monument in the square was dismantled. Every part of Shia society was targeted – mosques and religious meeting places were bulldozed. Frantic families searched for relatives who had disappeared into police and army custody and were not heard of for weeks.

Some human-rights activists were expecting to be arrested, but were amazed and shocked by the brutality with which they were treated. Zainab Abdul-Hadi al-Khawaja had suspected that her father, Abdul-Hadi al-Khawaja, a human-rights activist, would be detained and he had told his family he was willing to go voluntarily. Instead, a band of masked police broke into his house at 3am and dragged him downstairs, breaking his jaw as they did so. His interrogators continued to beat him on his fractured jaw and threatened him with rape unless he confessed. When Zainab saw him weeks later in military court, where he was sentenced to life imprisonment, his face was so badly swollen that he told his family: "I cannot even smile at you anymore."

Zainab and her father are among the few of those mistreated who are willing to say what happened on the record. Others gave me appalling accounts before saying anxiously: "Please don't give my name or any detail which would let the police know that I talked to you."

Any expression of sympathy for the protesters invited punishment. As Zainab was speaking to me in a coffee shop in Manama, the capital of Bahrain, a woman and child came to sit opposite us. The woman said she had worked for years in a government ministry dealing with the special needs of the disabled, but she had just been suspended. One count against her was that she had cried on the phone when talking to a senior official, saying: "It is wrong what is happening to the Shia in Bahrain."

Government officials and members of the Sunni community have a strikingly different picture of what happened in Bahrain. "There are almost totally different narratives," Bassiouni told me. Mariam Ahmed al-Jalahra, assistant under-secretary at the Ministry of Health, describes how the Salmaniya Medical Complex was taken over by doctors sympathetic to the protesters. "What happened was beyond disaster," she says, adding that patients were put in danger and had to be moved to other hospitals. She herself was stopped at the hospital gates by protesters, though she was allowed to proceed when her driver identified her as a doctor. "This was something scary," she says. She denies that any doctor is being punished for treating injured protesters, but says that those who broke rules should suffer sanctions.

What comes across in talking with Jalahra and other Sunnis is an exaggerated sense of victimhood in the face of mostly minor infringements of the law by the protesters. Two Sunni consultants from the 1,000-bed Salmaniya Medical Complex separately told me that they were very worried that they had been put on a "shame list" because they disagreed with fellow doctors, almost all Shia. Again there is a lack of a sense of proportion.

When I asked Sunni doctors what they thought of allegations, for which there is strong evidence, that their Shia colleagues have been tortured, they replied blandly that the matter was under investigation and, in any case, they doubt that mistreatment in prisons is as bad as was reported.

What did the interrogators want to find out from the consultants at Salmaniya which led to them being mistreated so badly? One doctor, still in detention, told his wife that he had been compelled to stand up for three weeks so the blood vessels and veins in his legs compacted. In miniature, the interrogators behaved like their predecessors during the show trials in Moscow in the 1930s, determined to extract confessions by any means that would support the unlikely official narrative of foreign-inspired plots and conspiracies. "It was bizarre," said one consultant who was badly beaten over four days. "They wanted to prove all the violence came from the protesters or the hospital. They wanted us to say that we had taken blood from the hospital blood bank and thrown it over protesters to exaggerate their injuries."

Finding evidence that the hospital and its staff were somehow linked to Iran was a priority. In one room in Salmaniya the police found a device they said came from Iran and was worth 52,000 dinar (£84,475), according to a price tag still on it. "They could not say what the device was for, but they kept saying it was collecting information for the Iranians," said the consultant.

Many doctors and teachers have now been released but others have been sentenced or are confined without charge. These include Rula al-Saffar, the head of the Nursing Society, and Jalila al-Salman, of the Bahrain Teachers' Society, who are both now on hunger strike. A further 2,500 people have been sacked, often with no reason. Almost all of them are Shia.

"What we are witnessing is sectarian cleansing," says Nabil Rajab, head of the Bahrain Centre for Human Rights. "We are being treated as an occupied people. It is exactly as in Israel. The government is trying to change the demography of the state. They may reduce the Shia to 40 per cent of the population, but they will become more extreme."

The Shia leaders' fear of government plans to marginalise their community may be exaggerated. The royal family seems to have panicked in March as long-established regimes fell across the Arab world. "They didn't need to bring in the Saudis," says Rajab. "No Shia home in Bahrain was left unaffected." Later I went with Rajab to the home of Abdul-Aziz Juma Ayad, a 38-year-old soldier who had been 20 years in the army and had died while under detention. His family said he had refused to act as an army sniper at Pearl Square and had been tortured with electric shocks to make him say he was importing weapons from Iran.

The Khalifas are in a strong military position. The army and police are dominated by Bahraini and foreign Sunni. The ruling elite is backed by Saudi Arabia, which is frightened of Shia dissent spreading to the Shia of its eastern province. The US has demanded the government moderate its repression, hinting that it might move its Fifth Fleet from its Bahrain base to somewhere else in the Gulf, but this sounds like an empty threat.

By targeting the Shia community and deepening its sense of alienation, the government is institutionalising instability on the island. The little state will become more reliant on Saudi Arabia and, as in Belfast or Beirut, religious loyalties and divisions will determine life and politics. Is it too late for the consequences of arrests, torture, killings, sackings and mosque demolitions to be reversed by government-backed conciliation? This might still just be possible but the genie of sectarian conflict, once released, never returns easily to its bottle.