The group of 335 workers were flown on a chartered Sri Lankan Airlines plane from Damascus, IOM spokeswoman Ranjitha Balasubramanyam said.
More Sri Lankan nationals were due to arrive back home later Saturday from Latakia, 350 kilometres (218 miles) northwest of the Syrian capital, after being transported there by bus from Beirut, Balasubramanyam said.
A first group of 276 people returned to Colombo last weekend from Lebanon.
Sri Lanka, which has more expatriate workers in Lebanon than any other country, has urged its nationals to stay put but said those who want to return will be brought back.
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"We are not encouraging them to come back. In fact, we want them (those who have already returned from Lebanon) to go back," Labour Relations and Foreign Employment Minister Athauda Senevirathne told reporters here Tuesday.
Some 1.2 million Sri Lankans work abroad, mainly in the Gulf states, and last year sent home 1.5 billion dollars.
Foreign remittances are the biggest foreign exchange ear