The year 2009 began with shocking photographs and video footage showing Thai officials allegedly mistreating Rohingya refugees, who had escaped neighbouring Burma by sea. The images were accompanied by stories of abuse, including allegations that Thai soldiers set refugees adrift in boats without engines. Reports in January 2009 indicated that as many as 200 Rohingya were missing, while 300 were known to have drowned. Boats full of refugees were found drifting in the Andaman Sea by the Indian Coast Guard. One survivor told IRIN, the UN news service, that Thai soldiers bound the hands of 412 refugees behind their backs, towed them out to sea and left them there. Another refugee, one of only 107 people to survive the ordeal, told IRIN, 'The food and water ran out within a few days. We were starving for nearly two weeks and feared we would never see dry land again.'

Chris Lewa, of the Arakan Rohingya National Organization, said in an interview that four boats containing at least some Rohingya refugees were found by Indian authorities in 2009, three of which had been set adrift by the Thai navy. The persons on board numbered 448 and included Bangladeshis as well as Rohingyas. At the end of 2009, Lewa said 224 Rohingyas remained in a prison in Port Blair in the Andaman Islands, which are administered by India. Seventy-nine Rohingya refugees remained in a detention centre in Bangkok. They were found on 19 August 2009 drifting in a boat with a broken engine and were picked up by the Thai navy. The refugees had first been caught by the Burmese navy, tortured and set adrift, according to Lewa. She said some of them had been burned and two of the refugees spent two months in the hospital recovering from the torture. Thai officials first put the refugees in a detention centre in Ranong, a province along the Andaman Sea, where conditions had been very poor. They were brought to Bangkok after human rights groups protested.

On 20 January 2009, the head of Thailand's army announced that the military would investigate the scandal, IRIN and other news agencies reported. Thailand said the probe would be led by the Internal Security Operations Command (ISOC), which is the same army unit that allegedly perpetrated the abuses. The ISOC was set up during the Cold War to run anti-communist death squads, according to IRIN. Thailand refused offers from outside agencies, including UNHCR, to help with the investigation. A year later, no details had been released to the public and it is unclear whether the ISOC had carried out an internal investigation.

The year ended with the Thai authorities targeting another refugee minority. On 28 December, the military deported more than 4,000 Hmong asylum-seekers to Laos, despite protests by human rights groups who accused the Laos government of human rights violations. Military units in riot gear forced thousands at the Huay Nam Khao refugee camp onto buses and sent them back to Laos. The Thai military had prevented UNHCR officials from entering the Huay Nam Khao refugee camp to assess their refugee claims. In May 2009, the international medical relief NGO Médecins Sans Frontières (MSF), which was the primary group providing medical aid to the refugees, withdrew from the camp in protest at the strong-arm tactics by Thai authorities. In a statement, MSF said, 'We can no longer work in a camp where the military uses arbitrary imprisonment of influential leaders to pressure refugees into a 'voluntary' return to Laos, and forces our patients to pass through military checkpoints to access our clinic.'

At a camp in Non Khai, 158 Hmong were also deported, despite UNHCR warnings that they were 'persons of concern' and could face persecution. The 158 who were detained in Non Khai had been granted refugee status. Kitty McKinsey, UNHCR's regional spokesperson, said in an interview, 'The fact that we gave them refugee status shows that they had a well-founded fear of persecution.' The governments of Australia, Canada, the Netherlands and the US had all volunteered to resettle the group, but the Thai government ignored the offers.

The Lao government has a history of animosity toward the Hmong because of their cooperation with the United States during its 'secret war' in Laos in the 1960s and 1970s. The US Central Intelligence Agency (CIA) recruited Hmong people in its fight against the communist Pathet Lao. Tens of thousands of Hmong fled after the US pulled out in 1975 and the Pathet Lao took over the country. The Hmong who were deported back to Laos on 28 December 2009 had arrived in Thailand in 2004, claiming they were fleeing persecution.

Thailand is home to about 150,000 refugees, according to Refugees International (RI), many of whom are ethnic minorities who fled Burma to nine camps on the Thai side of the border. Aid workers and UNHCR officials at the Mae La camp reported during 2009 that women suffer from high levels of domestic and sexual abuse, a situation that is likely to be similar in other camps. About 13,000 refugees from the camps were resettled in 2009, while more than 43,000 were resettled in 11 countries between 2004 and 2008, according to the UN. In a September 2009 report, RI warned that more funding for refugee camps might be necessary in 2010 if the Burmese military continues its offensive against ethnic militias, causing more refugees to flee to Thailand.

In southern Thailand, the military continued to fight an ethnic Malay armed group, and the number of attacks by the latter increased in 2009 compared to 2008. Malay Muslims are a minority in Thailand as a whole, but a majority in the southern provinces bordering Malaysia. The International Crisis Group (ICG) released a report in December 2009 which stated:

'Buddhist monks required military escorts and one was killed in a June bombing while another was injured; there were six car bombs during the first 11 months of the year, the highest number since 2004; by September 415 people were killed and 773 injured; most civilians who were attacked were those thought to be collaborating with the Thai authorities, especially teachers who, insurgents believe, are imposing Buddhist ideas on Malay Muslim students; by August nine educators had been killed; insurgents burnt down 11 schools in 2009.'

Muslims too came under attack in southern Thailand during 2009. On 8 June, gunmen opened fire on dozens of Muslims praying at a mosque in Aipayae village, killing 10 people and injuring 12. Police issued warrants for a former paramilitary ranger and another man – both Buddhists. Police said they believed the attack was in retaliation for the killing of Buddhists by insurgents. A video posted online in January 2009 showed a Malay Muslim man being beaten by Thai soldiers. Human rights groups documented three cases of serious abuse against Malay Muslims by security forces in 2009, and many less violent cases, according to ICG. The armed opposition group is thought to use terror tactics against fellow Muslims to keep them under control. On 12 March, for example, an insurgent shot and killed Laila Paaitae, a well known Muslim women's rights and peace activist who promoted coexistence between Malay Muslims and Thai Buddhists, HRW reported.

ICG accused the Thai government of failing to live up to promises to solve the conflict. In its December report, it said, 'The government has made little progress in addressing political grievances or alleviating the sense of injustice among Malay Muslims.' ICG recommended that the government take control of policy away from the military, including measures such as revoking martial law, which gives the military sweeping powers, as well as taking stronger measures to prosecute those responsible for attacks against Muslims, especially the 8 June attack on the mosque. ICG also recommended pursuing talks with the insurgents to explore options for a compromise, which could include 'a special administrative structure' for at least parts of southern Thailand.

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