Assad's regime has been battling an uprising that has come to be dominated by Islamists, ranging from moderates to radicals, who want to see Syria run as an Islamic state.
"The project of political Islam has failed, and there should be no mixing between political and religious work," he said in comments on the 67th anniversary of the founding of his Baath party.
Assad refers to all those fighting against him as "terrorists" and has said that he is battling extremists with retrograde ideas.
Assad said his government was also "continuing with the process of reconciliation, because what concerns us is ending the bloodshed and the destruction of infrastructure".
In recent months, Assad's government has negotiated limited ceasefires with rebels who agree to raise the government's flag in their neighbourhoods, and in many cases turn over their weapons.
The deals usually follow months-long sieges by the army, which have contributed to humanitarian crises in parts of the country.
Syria's conflict, which began in March 2011, has left more than 1,50,000 people dead.
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