Within days, the United States and Britain had "suspended" all deliveries of non-lethal materials to the supreme military council through Turkey. Although the FSA's chief of staff Salim Idris and his aides have tried to play down the incident - claiming the warehouses were taken in agreement with him, and denying reports he had fled the country - the events mark a worrying turn.
"The situation in the north now is very complicated and very dangerous, because there are some problems between some groups, and I think we should try everything to find a solution," Idris said last week.
His comments follow a warning he delivered last month to the US broadcaster PBS, when he accused jihadi groups of "fighting against" the Free Syrian Army. "They are trying to control the territories, which we liberated before. And they don't fight against the regime. And they are, for us, very dangerous."
The new Islamic Front can muster about 45,000 fighters, three times as many as the FSA. In a conflict in which the tide has been turning in favour of Bashar al-Assad, the balance of power has been shifting also among opposition groups, in favour of well-armed Islamists, some allied to al-Qaeda and supplied by wealthy donors in Qatar and Saudi Arabia, at the expense of the FSA.
The shift comes amid warnings from counter-terrorism experts that the two main al-Qaeda-affiliated groups - Jabhat al-Nusra and the rival Islamic State of Iraq and Syria (Isis) - are now better established in Syria and pose a greater threat than al-Qaeda in Iraq at the height of its strength there in 2006-07.
Writing in the journal of the Combating Terrorism Centre at West Point, Brian Fishman argued: "Jabhat al-Nusra and the Isis have more safe havens than [al-Qaeda] had in Iraq. The Syrian military has been denied access to vast swathes of Syria for months ... Those safe havens mean that [the two groups] can mitigate their ideological extremism through better training, and foreign fighters can be vetted and trained more thoroughly because they are less of a security hazard than foreign fighters were in Iraq."
Equally concerning for diplomats pushing for progress at next month's Geneva II conference is that rival groups and individual brigades competing for territory and influence is making it harder to achieve consensus, not least because some Islamist groups have rejected the conference.
Their agendas also differ. While Jabhat al-Nusra is in the van of the fight against the regime, Isis - analysts and rivals charge - has been more interested in consolidating its grip on territory it controls and establishing its own governance.
The formation last month of the Islamic Front, a grouping that has united tens of thousands of fighters from some of Syria's most powerful Islamist groups has provoked suggestions its emergence has undermined the authority and influence of the FSA. Although British and US diplomats were insisting last week the FSA - and Idris - were still the key force to be reckoned with, there were increasing signs of pressure to recognise changing circumstances.
Former diplomat Ryan Crocker, who has served in Syria, Iraq and Afghanistan, told the Washington Post, the US will need to deal with Assad. "We need to start talking to the Assad regime again" about counter-terrorism and other issues of shared concern, the paper reported, adding: "It will have to be done very, very quietly. But bad as Assad is, he is not as bad as the jihadis."
What is already happening is talks with more moderate groups in the Islamic Front, which reportedly took place in Turkey, headed by US envoy Robert Ford. That saw Syrian rebels say they were ready to include Islamist fighters as part of their delegation to the Geneva talks. Among those sceptical about the UK policy of backing the FSA as key representative is Jane Kinninmont of the foreign policy think-tank Chatham House.
"I speak to people who say the role of the jihadis is exaggerated because of their strategy of capturing areas close to the borders to control arms and supplies, and who say the FSA is still stronger deeper inside the country. But the latest news is a bad sign. You get the sense the UK in particular is in a bit of a bind about having backed the FSA so strongly."
She argues other factors are converging that will make the conference more difficult, including the fury of Saudi Arabia over the US nuclear deal with Iran. "Assad ... has presented himself as a partner with the West in getting rid of his chemical weapons, and is promising elections. With rising concern over the Islamist factions, and no prospect of outside military intervention, the levers that could be used to remove him are disappearing."
- Observer
