ANTAKYA, Turkey — It appeared to be a huge step forward for the scattered rebel groups fighting to topple President Bashar al-Assad of Syria: the creation of a central body of top insurgent commanders who would coordinate military campaigns, direct foreign support and serve as a unifying force for their diverse movement.

But 14 months after its creation, the body, known as the Supreme Military Council, is in disarray. Islamist groups have seized its weapons storerooms, its members have stolen or sold its supplies, and one prominent commander it armed and equipped has publicly joined an offshoot of Al Qaeda.

The council’s full dysfunction spilled into public view recently when a group of its members decided at a secret meeting to oust its chief of staff, Gen. Salim Idris, and put another man in his place.

While the opposition’s exiled leadership, the Syrian National Coalition, quickly congratulated the new leader, the move baffled many in the opposition, including the new leader himself, who had not even known he was in the running for the top job.