Last December, the Southeast Asian country accepted the first batch of 11 Syrian migrants who had relatives in Malaysia.
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Deputy Prime Minister Zahid Hamidi said the Syrian migrants, who flew into Malaysia via Lebanon, will be allowed to work while the children will be able to attend public schools.
"Malaysia will take in 3,000 Syrian refugees," he told reporters after the arrival of the second batch of migrants.
"About 200 more will be coming in the next few months," he said.
Zahid said they will be provided with accommodation and financial assistance during their "temporary" stay, with local NGOs providing humanitarian support.
As the refugees stepped out of the aircraft and onto the tarmac at the Subang Air Force base, west of capital Kuala Lumpur, they smiled as they clutched their belongings and their children.
Last October, Prime Minister Najib Razak said Malaysia would accept 3,000 Syrian migrants over the next three years to help ease the refugee crisis.
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Europe is facing a strain with the influx of hundreds of thousands of people fleeing Syria and other countries who are seeking asylum.
Malaysia, however, is not a signatory to the UN's key refugee treaty hence there are no laws to protect refugees though it accepts them temporarily.
Refugees are considered illegal immigrants and are not allowed to seek employment.
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