"Terrorist groups have kidnapped five Syrian drivers and six members of the Organisation for the Prohibition of Chemical Weapons (OPCW) team investigating the use of chlorine gas," the ministry said.
The team have been investigating allegations that Syrian government forces unleashed the industrial chemical on a rebel-held village in Hama province last month.
There was no immediate comment on the reported abduction from the OPCW.
The ministry said the team went missing as they were travelling in two vehicles from government-held Teebet al-Imam to rebel-held Kafr Zita, the scene of the alleged attack.
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The Syrian government signed the convention last year as part of a Russian- and US-brokered deal under which it pledged to destroy all of its chemical arsenal.
Syria was not required to declare its stockpile of chlorine -- a toxic but weak agent -- as it is widely used for commercial and domestic purposes.
But its use for military purposes would still be a breach of Damascus's undertakings under the convention.