The removal was carried out as the head of Al-Qaeda's Syria affiliate, the Al-Nusra Front, called for an end to four days of clashes between rebels and the jihadist Islamic State of Iraq and the Levant in which at least 274 people were killed.
"A first quantity of priority chemical materials was moved from two sites to the port of Latakia for verification and was then loaded onto a Danish commercial vessel today," the joint United Nations-Organisation for the Prohibition of Chemical Weapons (UN-OPCW) mission said in a statement.
The removal of the chemical material from Syria's coastal Latakia comes after a planned December 31 deadline for the operation to begin was missed.
Today's shipment "initiates the process of transfer of chemical materials from the Syrian Arab Republic to locations outside its territory for destruction," the UN-OPCW statement said.
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The material taken from Syria today will be held at sea until additional chemicals arrive. The shipment is being escorted by Chinese, Danish, Norwegian and Russian vessels, the mission said.
Syria agreed last year to a US-Russian deal to hand over its chemical weapons.
Under the plan, the chemicals taken from Latakia will be transported to an Italian port and transferred onto a US vessel, where they will be destroyed.
The mission has a June deadline to complete the dismantling of Syria's chemical weapons programme, which includes the deadly nerve agent sarin and mustard gas.
At OPCW headquarters in the Hague, director-general Ahmet Uzumcu said the first removal was an "important step".