Patrick Cockburn: Bahrain is trying to drown the protests in Shia blood

"Let us drown the revolution in Jewish blood" was the slogan of the tsars when they orchestrated pogroms against Jews across Russia in the years before the First World War. The battle-cry of the al-Khalifa monarchy in Bahrain ever since they started to crush the pro-democracy protests in the island kingdom two months ago might well be "to drown the revolution in Shia blood". Just as the tsars once used Cossacks to kill and torture Jews and burn their synagogues, so Bahrain's minority Sunni regime sends out its black-masked security forces night after night to terrorise the majority Shia population for demanding equal political and civil rights.

Usually troops and police make their raids on Shia districts between 1am and 4am, dragging people from their beds and beating them in front of their families. Those detained face mistreatment and torture in prison. One pro-democracy activist, Abdulhadi al-Khawaja, brought before a military court last week with severe facial injuries, said he had suffered four fractures to the left side of his face, including a broken jaw that needed four hours' surgery.

The suppression of the protests came after Saudi Arabia and the Gulf Co-operation Council – also known as the "kings' club" of six Gulf monarchs – sent 1,500 troops to Bahrain to aid the crackdown, which began on 15 March. It soon became clear that the government is engaged in a savage onslaught on the entire Shia community – some 70 per cent of the population – in Bahrain.

First came a wave of arrests with about 1,000 people detained, of whom the government claims some 300 have been released, though it will not give figures for those still under arrest. Many say they were tortured and, where photographs of those who died under interrogation are available, they show clear marks of beating and whipping. There is no sign yet that King Hamad bin Isa al-Khalifa's declaration that martial law will end on 1 June is anything more than a propaganda exercise to convince the outside world, and foreign business in particular, that Bahrain is returning to normal.

The repression is across the board. Sometimes the masked security men who raid Shia villages at night also bulldoze Shia mosques and religious meeting places. At least 27 of these have so far been wrecked or destroyed, while anti-Shia and pro-government graffiti is often sprayed on any walls that survive.

The government is scarcely seeking to conceal the sectarian nature of its repression. Defending the destruction of Shia mosques and husseiniyahs (religious meeting houses), it claims that they were constructed without building permission. Critics point out that one of them was 400 years old. Nor is it likely that the government has been seized with a sudden enthusiasm for enforcing building regulations since the middle of March.

The government is determined to destroy all physical rallying points for the protesters. One of the first such places to be destroyed was the Pearl Square monument, an elegant structure commemorating the pearl fishers of the Gulf, which was bulldozed soon after the square had been cleared of demonstrators. A measure of the government's paranoia is that it has now withdrawn its own half-dinar coins showing the iconic Pearl Square monument.

Facing little criticism from the United States, so concerned about human rights abuses in Libya, the al-Khalifa family is ruthlessly crushing opposition at every level. Nurses and doctors in a health system largely run by Shias have been beaten and arrested for treating protesters. Teachers and students are being detained. Some 1,000 professional people have been sacked and have lost their pensions. The one opposition newspaper has been closed. Bahraini students who joined protests abroad have had their funding withdrawn.

The original 14 February protest movement was moderate, contained Sunni as well as Shia activists, and went out of its way to be non-sectarian. Its slogans included demands that Bahrain's powerful prime minister for the past 40 years, Sheikh Khalifa bin Salman al-Khalifa, step down and for fair elections. It also wanted equal rights for all, including an end to anti-Shia discrimination under which the majority were excluded from joining the 60,000-strong army, police and security forces. Security jobs went instead to Sunni recruits from Pakistan, Jordan, Syria and other Sunni states who were immediately given Bahraini citizenship.

Sometimes the anti-Shia bias is explicit. One pro-government newspaper prominently published a letter that compared the protesters to "termites", which are intelligent but multiply at alarming speed, and "are very similar to the 14 February group that tried to destroy our beautiful, precious country." The writer recommends exterminating the "white ants so they don't come back".

The purpose of the systematic torture and mistreatment inflicted on the detainees is first to create a feeling of terror in the civilian population. It is not only protesters or pro-democracy activists that are being targeted. Al-Jazeera satellite television, based in and funded by neighbouring Qatar, which played such a role in publicising protests and their attempted repression in Tunisia, Egypt, Syria, Yemen and Libya, was initially much more reticent about reporting events in Bahrain. But al-Jazeera revealed this week that the Bahraini police have been raiding girls' schools, detaining and beating schoolgirls, and are accused of threatening to rape them.

One 16-year-old called "Heba" was taken with three of her schoolfriends and held for three days, during which they were beaten. She said an officer "hit me on the head and I started to bleed" and she was thrown against a wall. Although the girls were beaten severely, she said, they scarcely felt the pain because they were so frightened of being raped. The Bahraini opposition party Al Wefaq says that 15 girls' schools have been raided by the police and girls as young as 12 threatened with rape.

Aside from intimidation there is a further motive for the beatings and torture: namely, to extract evidence that, against all appearances, the opposition is planning armed revolt and is manipulated by foreign powers, notably Iran. The aim, in the case of Abdulhadi al-Khawaja, was evidently to beat out of him a confession that he was attempting to "topple the regime forcibly in collaboration with a terrorist organisation working for a foreign country".

The al-Khalifas are aware that their strongest card in trying to discredit the opposition is to claim it has Iranian links. US embassy cables revealed by Wikileaks show that the Bahrain government was continually making this claim to a sceptical US embassy over the years, but has never provided any evidence. This propaganda claiming Iranian plots is crude, but plays successfully in Sunni Gulf states that see an Iranian hand behind every Shia demand for equal rights and an end to discrimination. It also gets an audience in Washington, conscious that its Fifth Fleet is based in Bahrain and fearful of anything that could strengthen Iran.

The Bahraini monarchy, having effectively declared war on the majority of its own people, is likely to win in the short term because its opponents are not armed. The cost will be that Bahrain, once deemed more liberal than its neighbours, is turning into the Gulf's version of Belfast or Beirut when they were convulsed by sectarian hatred.