The report by the Organisation for the Prohibition of Chemical Weapons (OPCW) was released on Wednesday to the UN Security Council, which is overseeing efforts to dismantle Syria's chemical weapons program.
Syria has agreed to destroy seven aircraft hangars and five underground structures identified by the OPCW as chemical weapons production sites but there have been delays caused by logistical problems.
In the report obtained by AFP, OPCW director general Ahmet Uzumcu said his team of experts was able to verify that three tunnels have been destroyed and that work on dismantling a fourth underground structure was under way.
"Currently, one underground structure and two hangars are not accessible owing to the security situation near these sites," he wrote in the report dated March 23.
Despite this hurdle, Uzumcu said he expected the destruction of all five underground tunnels to be completed by June.
Concerning the hangars, work has begun on five sites and explosives are to be delivered soon to begin demolishing the structures.
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"The Syrian authorities have continued to extend the necessary cooperation" for the dismantling of the 12 sites, the report added.
The Security Council is due to discuss progress in dismantling Syria's chemical weapons program at a meeting on April 2.
Syria finished disabling the production sites by October 2013, however the structures that house them still needed to be destroyed.
After an August 2013 sarin attack outside Damascus that much of the international community blamed on President Bashar al-Assad's government, the regime agreed to turn over its chemical arsenal.
The United States threatened military action against Damascus over the attack, but held off following the chemical disarmament agreement.
A total of 1,300 metric tonnes of chemical weapons have been removed from Syria, with the majority being destroyed aboard the US Navy ship MV Cape Ray.