Syrian rebels freed 48 Iranian hostages on Wednesday in exchange for the release of more than 2,000 civilian prisoners held by the Syrian government, the head of a Turkish aid agency which helped broker the deal said.

The Syrian rebel al-Baraa brigade seized the Iranians in early August and initially threatened to kill them, saying they were members of Iran's elite Islamic Revolutionary Guard Corps sent to fight for Syrian President Bashar al-Assad.

The Islamic Republic, one of Assad's closest allies, denied this, saying they were Shi'ite pilgrims visiting shrines, and it asked Turkey and Qatar to use their connections with Syrian insurgents to help secure their release.

"The 48 Iranians have been released and are being taken to Damascus, accompanied by Iranian and Syrian officials," Bulent Yildirim, the head of humanitarian aid agency IHH, told Reuters by telephone from Damascus.

He said the release of 2,130 civilian prisoners, most of them Syrians but also including Turks and other foreign citizens, had begun in return. Two state-run Iranian television channels also reported that 48 Iranians had been freed in a swap.

There was no confirmation from the Syrian government, which has periodically freed hundreds of prisoners over the 21-month-old conflict in apparent concessions. But Damascus has always stressed such prisoners "do not have blood on their hands."

Syrian government forces have struck local deals with rebel groups to trade prisoners but the release announced on Wednesday would be the first time non-Syrians were freed in a swap.

Opposition groups accuse Assad of detaining tens of thousands of political prisoners during his 12 years in office and say those numbers have spiked sharply during the civil war.

Missing persons became a key issue when street protests against Assad first erupted in March 2011.

Turkey is one of Assad's fiercest critics, a strong opposition backer and proponent of international intervention. It has been highly critical of Iran's stance during the Syrian uprising, which has killed around 60,000 people according to a UN estimate.

Turkey, Gulf states, the US and European allies support the mainly Sunni Syrian rebels, while Iran supports Assad, whose Alawite minority is an offshoot of Shi'ite Islam.-Reuters