In a statement posted on Facebook on Friday, the defence ministry said the group's leader in Deir Az Zor and its "minister of war" were among those killed in the attack.
"As a result of a precision air strike of the Russian air forces in the vicinity of Deir Az Zor city, a command post, communication centre and some 40 ISIS fighters have been kille,d including Deir Az Zor emir Abu Mohammed al-Shimali," the ministry said.
Gulmurod Khalimov, a native of Tajikistan, who is known as the armed group's minister of war, suffered a "fatal injury", the ministry added.
Khalimov received US training and headed the Tajik interior ministry's special forces unit before joining ISIL in 2015.
The Russian defence ministry said the air attack, which was carried out on an unspecified date, was ordered after Moscow received intelligence earlier this week about a meeting of senior ISIL commanders in the area.
Backed by Russia, Syrian troops on Tuesday broke through a years-long siege imposed by ISIL fighters on tens of thousands of civilians in Deir Az Zor.
Heavy clashes are taking place between Syrian government forces and the armed group around the city as ISIL fights back to reinstate a years-long siege of the city.