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The violence between Kyrgyz and Uzbek residents in the southern cities of Osh and Jalalabad began late on Thursday and escalated over the weekend. Witnesses said gangs with automatic rifles, iron bars and machetes had set fire to houses and shot fleeing residents.
Some 100,000 ethnic Uzbeks have fled to the nearby border with Uzbekistan or sought refuge in local villages to escape the deadliest fighting in two decades. Many said they were being targeted by Kyrgyz gangs in a "genocide" backed by local police and troops.
"Crowds of Kyrgyz are roaming around, they set our homes on fire and kill Uzbeks right in their houses," ethnic Uzbek Muhammed Askerov, a Jalalabad businessman, told Reuters by telephone.
It is unclear what triggered the clashes. Some officials have pointed to a conflict at a local casino or rumors of a dispute sparked by a taxi passenger who declined to pay his fare. Others have spoken of Kyrgyz girls being raped by Uzbeks.
The ethnic violence raises the risk of a civil war or even a full-blown conflict between Kyrgyzstan and Uzbekistan. If the interim government loses control, Kyrgyzstan could disintegrate and cease to exist as a single independent country.
Moscow sent at least 150 paratroopers to Kyrgyzstan on Sunday to protect its own military facilities in the country and representatives of the Moscow-led security bloc of ex-Soviet republics known as the Collective Security Treaty Organization (CSTO) gathered on Monday to discuss further steps.
"We have gathered here to discuss the situation in Kyrgyzstan and discuss the ways to solve this crisis, to restore order, to stop the interethnic conflict," Russia's national security chief Nikolai Patrushev was quoted by RIA Novosti news agency as telling the meeting.
"Today we have to work out a common position and concrete measures to react to the situation in Kyrgyzstan based on a CSTO mandate."
The CSTO comprises Russia, Belarus, Armenia, Kazakhstan, Kyrgyzstan, Tajikistan and Uzbekistan.
Kyrgyzstan's interim government, which assumed power after an April revolt that overthrew president Kurmanbek Bakiyev, has been unable to gain full control of the country's south, which is separated from the north by mountains.
The renewed turmoil in Kyrgyzstan has fuelled concern in Russia and the United States.
Washington uses an air base at Manas in the north of the ex-Soviet state, about 300 km from Osh, to supply forces in Afghanistan. Russia also has a military base in the country.
A Reuters witness in Osh said gangs resumed shooting on Monday at residents and homes in one area of Jalalabad. Uzbeks who fled the city accused authorities appointed by the interim government of aiding ethnic Kyrgyz in carrying out genocide.
"Their slogan is 'Kyrgyzstan for Kyrgyz', and officials and police act hand-in-glove with them," the Jalalabad businessman Askerov said. "But our ancestors were born here. Where should we go?"
Reuters contributed to the story.