Witnesses say the team of experts left their Damascus hotel in the early hours of Sunday, heading for an unknown location.
The group consists of experts from the Organisation for the Prohibition of Chemical Weapons (OPCW) in The Hague and United Nations officials assisting them.
The inspectors arrived in Damascus on Tuesday to start their mission, which was arranged by Washington and Moscow after an August 21 chemical weapons attack in Damascus prompted US threats of air strikes.
The mission is expected to continue until at least mid-2014 with the Syrian government and the rebels blame each other for the chemical incident in a Damascus suburb in which 1400 people were killed.
The United States and other Western countries say a report by UN investigators indirectly implicates government-allied forces with the attack.
United Nations peace envoy for Syria, Lakhdar Brahimi, has repeated his statement that peace talks could take place in November in Geneva.
Asked if the conference was a certainty, he said in an interview with TV5 television: “No, this is not a certainty. I am trying to invite…I am encouraging everybody to come to Geneva in the second half of November.”