"Everybody is now acting in its own way," René Rouquet said in regard to combatting the Islamic State.
"It will be more efficient that everyone acts together, but the difficulty is the position on Assad," Rouquet added.
The United States, its Western allies and a number of Syria’s regional rivals, advocate the removal of Assad from power as a key way forward in resolving the ongoing civil war and humanitarian crisis. Russia, on the other hand, backs Assad as the legitimate authority of the Arab republic.
In his address to the 70th United Nations General Assembly on Monday, Russian President Vladimir Putin said it is an "enormous mistake" to refuse to cooperate with the Syrian government in its anti-ISIL efforts.
Russia has recently established a joint center in the Iraqi capital of Baghdad to coordinate efforts to tackle IS with Iran, Iraq and Syria.
The French air force conducted its first airstrikes against IS positions in Syria on Sunday.