Supreme Military Council leader Selim Idriss pledged cooperation, however, with a newly formed alliance of Islamist rebel groups just days after it committed itself to setting up an Islamic state in Syria.
His comments, in an interview with the Dubai-based Al-Aan news channel, come amid a mounting outcry at beheadings and other summary executions carried out by fighters loyal to Al-Qaeda who have become a significant force on the ground.
But "there are those who come from abroad, and we know nothing about them... Who want to impose on us customs... labelling people either Muslim or atheist, heretic and worthy of beheading.
"This is foreign to us, and to the moderation... Of the Islam that we want to hold on to," Idriss said in excerpts of the interview obtained by AFP.
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"I... Congratulate and bless our brothers in this front," Idriss said, adding: "A large number of the brothers in this front are with us in the Supreme Military Council."
Some but not all of the factions in the Islamic Front are nominally loyal to Idriss's SMC, the military arm of the opposition National Coalition recognised by many Arab and Western governments.
The SMC has struggled to exert control over the myriad of rebel units, something Idriss attributed to the failure of foreign governments to provide it with adequate supplies of weaponry to channel to fighters on the ground.