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 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.
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 is the strongest sign yet the U.S.-allied FSA armed opposition structure is crumpling under extremist pressure, the Journal said.
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.