Dalil Boubakeur said "99.9 percent" of Muslims in France are law-abiding citizens and that the killings of three soldiers, three Jewish children and a rabbi in the Toulouse region were the work of a tiny "fringe".
Boubakeur said he and other religious leaders had been invited to meet President Nicolas Sarkozy at the Elysee Palace later in the morning, to discuss community relations in the wake of the attacks.
The suspect, besieged by police in an apartment block in the southern city of Toulouse, is a 24-year-old French citizen of North African descent who has claimed to acting to "avenge Palestinian children" killed in the Middle East.
Interior Minister Claude Guéant said he has fired on police and was known to the DCRI intelligence agency as someone who had travelled to Afghanistan and Pakistan, where extremist groups have safe houses and training camps.
"I'm competely surprised that the author of these misdeeds be from a fundamentalist, jihadist, terrorist-type movement of the kind we thought was controlled, neutralised and harmless in our country," Boubakeur said.
"We understand the seriousness of this news ... because it is important not to mix this up with the Muslim religion, which is 99.9 percent peaceful, civic-minded, reasonable, non-violent and entirely integrated in our country."