"As we speak, the ship (carrying the last chemicals) has just left the port (of Latakia)," Ahmet Uzumcu, head of the Organisation for the Prohibition of Chemical Weapons, said at a press conference in The Hague.
"Removing the stockpile of precursor and other chemicals has been a fundamental condition in the programme to eliminate Syria's chemical weapons programme," Uzumcu said.
Syria had previously shipped out 92 per cent of its stockpile of chemical weapons under the terms of a UN-backed and US-Russia brokered agreement last year.
"We hope to conclude soon the clarification of certain aspects of the Syrian declaration and commence the destruction of certain structures that were used as chemical weapons production facilities," Uzumcu said.
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Under last year's agreement Syria had until the end of June for the destruction of its chemical weapons, but it has been widely acknowledged that the deadline would not be met.
The deal was reached after a sarin nerve gas attack in a rebel-held Damascus suburb killed around 1,400 people.
A Danish ship is now to take the chemicals to the US ship Cape Ray for destruction at sea, while some chemicals are to be destroyed at sites in Finland, the US and Britain.