The assertion came after the head of the Organisation for the Prohibition of Chemical Weapons said one abandoned site was in a rebel-held area and that inspectors from a UN-OPCW team were hoping to visit it.
In a statement, the Syrian National Coalition opposition grouping said it backed the UN-OPCW mission but insisted none of the weapons sites were under rebel control.
"There are chemical sites under regime control that Free Syrian Army brigades are laying siege to but there are no chemical sites at all that are controlled by the rebel brigades," the Coalition said.
The statement said the Coalition and rebel command sought "full cooperation with all international missions to facilitate their work and ensure their full protection."
On Monday, OPCW director general Ahmet Uzumcu told the BBC that inspectors from the mission had visited five out of at least 20 Syrian sites where chemical weapons could be produced.
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And he said one abandoned chemical weapons site was in rebel-held territory and that routes to other sites went through opposition-held areas.
The first members of the UN-OPCW team arrived in Syria on October 1 to carry out the terms of a UN Security Council resolution on the verification and destruction of Syria's chemical arsenal.
The resolution enshrined a US-Russian deal that came in the wake of an August 21 sarin attack on the outskirts of Damascus.
The United States threatened military action against the regime in response to the attack, despite the government's denial of responsibility.
But the threatened strikes were called off after the US-Russian agreement.