"It is better late than never, but are Turkish intentions to fight the terrorists of Daesh (IS), Al-Nusra Front, and Al-Qaeda-linked groups genuine?" the ministry asked in a letter to the United Nations.
The ministry said Syria "rejects the Turkish regime's attempt to paint itself as a victim that is defending itself", accusing Ankara of supporting "terrorist" groups.
The letter made no direct mention of Turkish air attacks in northern Syria, which began early Friday after Ankara claimed a Turkish soldier was killed in cross-border fire by IS jihadists.
Syria's regime has repeatedly accused the Turkish government of supporting "terrorists" - the word it uses to describe all armed groups opposed to Damascus.
The civil war raging throughout Syria began in March 2011 with anti-government protests, but has since devolved into a complex conflict.
The spectacular rise of IS prompted the US and its allies to begin an air campaign against the jihadist group in September 2014.
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