The FSA Higher Military Council replaced Idriss as its chief with Brigadier General Abdel Ilah al-Bashir on Sunday, citing the "difficulties” in their deadly war to change the government.
But several militant leaders have lashed out at the move, with some branding it an undemocratic "coup".
"We consider the removal of... Idriss an invalid, illegitimate decision," said a statement issued by all five top field commanders of the FSA's Supreme Military Council, which Idriss had led from December 2012.
In their statement, the commanders vowed to continue fighting the government of their country "under the leadership of General Selim Idriss" who was "elected democratically".
Idriss had been voted in by military councils on the ground.
Speaking to AFP on condition of anonymity, a well-connected militant in Syria said Idriss' removal was decided in a "secret meeting" by the Higher Military Council, which many key militants have abandoned in recent months.
"Regardless of Idriss' shortcomings, this is a military coup," said the militant.
"The main problem is: why weren't all the military councils called in to vote?"
Idriss had long faced criticism by militants on the ground for failing to gather sufficient military aid for the armed groups.
Also speaking on condition of anonymity, a FSA source on Wednesday blamed the shortcomings of Idriss' leadership on international backers of the war, which have mainly directed military aid to factions fighting on the ground rather than to Idriss.
"General Selim Idriss did everything he could to strengthen the (FSA)... The Supreme Military Council has in the past year received only $3 million in assistance" from backers of the war, said the source.
This was in addition to "some assistance from a Western country, which then stopped," the source added, without naming the country.
Syria sank into war in 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.
SHI/SHI