Brig. Gen. Mustafa al-Sheikh, who heads the FSA's Military Council, told The Associated Press that the move aims to unite all rebel groups. He said Saturday that the move was made the week before, without specifying its new location.
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FSA commander Col. Riad Asaad issued a video titled "Free Syrian Army Communiqué Number 1 from Inside" that the command has moved to "liberated areas."
The FSA has been the most prominent of the rebel groups trying to remove President Bashar Assad from power. But its commanders have come under criticism in the past for leading from Turkey, and its authority over numerous locally-based networks of fighters is limited.
Also on Saturday, rebel fighters trying to oust Assad reported shooting down a fighter jet as it flew over the northern Syrian town of Atarib in Idlib province.
An eyewitness, an independent journalist who asked to remain anonymous, said rebel fighters were attacking a military base near the town when the jet flew over and rebels shot it down with anti-aircraft guns.
Vastly outgunned, rebels said they need surface-to-air missiles to take down planes and helicopters used by the Syrian military to bombard opposition strongholds.
On August 27 fighters shot down a helicopter on the outskirts of Damascus and three days later rebels said they had brought down a jet in Idlib, near the Turkish border.
Activists say more than 27,000 people, mostly civilians, have been killed in the 18-month-old revolt in Syria.
Despite calling for Assad to step down, the West is wary of arming disparate rebel groups.
AP and Reuters contributed to this report
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