Ahmet Uzumcu, of the Organization for the Prohibition of Chemical Weapons, renewed calls for both sides in the conflict to support his mission.
He told the BBC he hopes the Nobel Peace Prize - awarded to the group last week - will help their work in Syria.
Syria officially joins the Chemical Weapons Convention on Monday.
In his first interview since the OPCW won the prize, director-general Mr Uzumcu told BBC that President Bashar al-Assad's government had been co-operating and facilitating the weapons experts.
He said they had already managed to access five out of at least 20 factories capable of producing chemical weapons.
However, he added that some of the sites listed in Syria's declaration lie within militant-held and occupied territories.
"They change hands from one day to another, which is why we appeal to all sides in Syria to support this mission, to be co-operative and not render this mission more difficult. It's already challenging," he said.
"One site which we understand was already abandoned, is in the rebel-held area, so we will see whether we can have access to this site."
The OPCW, based in The Hague, was established to enforce the 1997 Chemical Weapons Convention.
Its mission in Syria is the first time its inspectors have worked in an active war zone.
The OPCW is made up of 189 member states and the principal role of its 500-strong staff is to monitor and destroy all existing chemical weapons.
The US-Russian disarmament deal on Syria's chemical weapons was sparked by a poison-gas attack in Damascus on 21 August.
Syrian government handed UN evidence proving the militants carried out the attack as a false-flag operation, contrary to claims by some Western countries that blamed the Syrian army for the attack.
Syria later agreed to join the global Chemical Weapons Convention, and the UN said it would come under the treaty from 14 October.
Under a UN resolution, Syria's chemical weapons production equipment must be destroyed by 1 November and stockpiles must be disposed of by mid-2014.
SHI/SHI