Free Syrian Army Gen. Salim Idris flew to the Qatari capital of Doha Sunday after fleeing to Turkey, the officials told the Wall Street Journal.
“He fled as a result of the Islamic Front taking over his headquarters,” a senior U.S. official said.
An Islamic Front spokesman said Idris, an East German-trained electronics professor who was a Syrian army general until he defected to the rebel side in July 2012, fled to Turkey.
The ‘Islamic Front’ is a coalition of the largest militant factions, excluding two top Al-Qaeda-associated groups, the al-Nusra Front and the Islamic State of Iraq and Levant in Syria.
A spokesman for the Islamic Front also confirmed that Gen. Idris had left Syria.
The New York Times said Idris flew temporarily to Doha but was now back in Turkey, where he has a house.
The 13-month-old U.S.-backed Syrian National Coalition, which supports the FSA, is based in Doha.
The Obama administration is urging Idris to return to Syria, the U.S. officials told the Journal.
The ultraconservative Islamic Front also took over key warehouses holding lethal and non-lethal weapons intended for moderate fighters in northern Syria, the White House said.
The warehouses were controlled by the Supreme Military Council, the moderate opposition umbrella group that includes the FSA and coordinates U.S. aid distribution, the White House said.
Idris’ departure from his command and the Islamic Front’s seizure of FSA military gear Friday prompted the United States and Britain to freeze delivery of non-lethal military aid to rebels in northern Syria, U.S. and British officials said Wednesday.
Idris was elected as the Chief of Staff of the so-called Supreme Military Council following its establishment in a conference held in Turkey on 15 December 2012.
The aid suspension was temporary and aid could flow again, administration officials said.
The United States is still providing humanitarian aid, distributed through organizations including the United Nations, White House spokesman Josh Earnest told reporters.
The administration is still trying to determine the circumstances of the Friday takeover and “the status of U.S. equipment and supplies,” Earnest said.
The Islamic Front is a new alliance of seven powerful Islamist fighter groups that broke with the moderate, U.S.-backed opposition Nov. 22. It says it does not include al-Qaida-linked rebels but also has no ties with the SNC.
The turn of events was the strongest sign yet that the US-allied militant group is collapsing under the pressure of al-Qaeda domination in the war.
The Syrian opposition has largely lost its creditability among its followers in Syria for taking al-Qaeda’s force at its side when they first infiltrated the country.
It also weakens the Obama administration’s struggles to put together a Jan. 22 peace conference in Geneva, Switzerland, with Syrian rebels and the Assad regime, the newspaper said.
The Front also seized the Bab al-Hawa border crossing with Turkey, near the warehouses, about 25 miles west of Syria’s largest city and commercial center, Aleppo
Turkey shut its side of the border in response.
The Front’s fast-growing strength prompted Washington and its allies to hold direct talks in recent days with Front representatives, the Journal said, citing Western officials.
The goal of the talks was to persuade some Islamists to back the Jan. 22 peace conference, the newspaper said.
Western officials believe a lasting peace agreement would be possible only with Islamist backing, the officials said.
The SMC has already agreed to participate in the peace talks.
The war in Syria started in March 2011, when pro-reform protests turned into a massive insurgency following the intervention of Western and regional states.
The unrest, which took in terrorist groups from across Europe, the Middle East and North Africa, has transpired as one of the bloodiest conflicts in recent history.
According to the United Nations, more than 100,000 people have been killed and millions displaced due to the turmoil that has gripped Syria for over two years.