Chairman of FSA Joint Chiefs of Staff , Salim Idriss denied claims he fled Syria to Qatar, as the American Wall Street Journal reported.
"Such rumors are intended to weaken the morale of Free Syrian Army fighters," Idriss said.
WSJ said that Islamist fighters overran the headquarters of the top Western-backed rebel commander and that he fled the country, citing U.S. officials on Wednesday.
Idriss flew to the Qatari capital of Doha on Sunday after fleeing to Turkey, the U.S. officials reportedly said.
"He fled as a result of the Islamic Front taking over his headquarters," a senior U.S. official said to WSJ.
An Islamic Front spokesman also said Idriss had fled to Turkey.
Idriss told Zaman al-Wasl that he is regularly travelling for military and humanitarian purposes related to FSA armament and to mobilize support for Syrian revolution.
Islamists took over key warehouses holding U.S. military eqipment for moderate fighters in northern Syria over the weekend. The takeover and flight of Idriss shocked the U.S., which along with Britain, immediately froze delivery of nonlethal military aid to rebels in northern Syria, the WSJ said.
Idriss downplayed the U.S. decision to suspend aid non-lethal aid, saying it will not change the balance of power on the ground and will not affect combat operations, pointing out that that Washington has offered no more than communication devices, computers, military uniforms and some body armor. "It is not strategic weapons," he said.
The Joint Chiefs of Staff, in a statement issued last Friday, denied the claims its depots had been attacked by the Al-Qaeda affiliated Islamic State of Iraq and Greater Syria (ISIS) and the Islamic Front.
The Statement said the Chiefs had asked the assistance of the Islamic groups when its depots in Idleb province had been attacked by an armed group.
The Islamic Movement of Ahrar al-Sham has protected FSA officers who escaped death, as well it has secured the rest of the depots, a Zaman al-Wasl source said.
Translated and edited by The Syrian Observer