"No war weapons have been exported to Syria in 2013," Ismet Yilmaz said in parliament, according to media reports.
Hurriyet Daily News reported yesterday that Turkey had shipped 47 tonnes of weapons to Syrian rebels since June, citing UN and Turkish Statistics Institute documents.
Turkey is a fierce opponent of Syrian President Bashar al-Assad and has openly supported the rebels, but has always denied arming them.
Yilmaz said his ministry had not issued any permits for the export of military equipment to Syria in 2013.
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A powerful Islamist faction seized weapons warehouses on the Turkish border from the Western-backed Free Syrian Army earlier this month, highlighting concerns that Syria's moderate opposition may be in disarray.
The United States and Britain responded by suspending all non-lethal aid to the FSA.
Turkey, which has been accused of turning a blind eye to fighters crossing its border into Syria, is sheltering about 600,000 Syrian refugees who have fled the civil war as well as the main Syrian opposition group.