Organisation for the Prohibition of Chemical Weapons head Ahmed Uzumcu said his body's fact-finding teams have found evidence of the use of sulphur mustard in attacks in the two war-torn countries.
"Although they could not attribute this to Daesh... There are strong suspicions that they may have used it (chemical weapons)," Uzumcu told AFP, using the alternative name for the jihadist group.
"Secondly the suspicions are that they may have produced it themselves, which is extremely worrying," Uzumcu said on the sidelines of a three-day conference at the OPCW's Hague-based headquarters.
CIA director John Brennan in February told CBS News that IS fighters had the capability to make small quantities of chlorine and mustard gas.
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Uzumcu did not point to any specific attacks, but last month IS mounted a deadly gas attack against Syrian troops at a government-controlled airbase outside the divided eastern city of Deir Ezzor, according to the SANA state news agency.
The attack was the latest in a string of suspected mustard gas attacks by the jihadists in Syria and neighbouring Iraq.
While chemical agents allegedly used by IS so far have been among its least effective weapons, the psychological impact on civilians is considerable.
A total of 25,000 people fled their homes in and around Taza last month, fearing another attack.
Uzumcu also urged vigilance by other nations to guard against any chemical attacks outside Syria and Iraq.