The 32-year-old Dynamo Moscow midfielder underwent tests after complaining of discomfort following the 1-1 friendly draw with Serbia on Sunday.
And the Russian Football Union have subsequently issued a statement to confirm that Denisov will leave Leonid Slutsky's squad as he has no chance of being fit for any of the group games against England, Slovakia or Wales.
"On Monday, midfielder Igor Denisov underwent the MRT examination in Paris after the injury he got in the friendly match against Serbia," the statement said.
"The examination confirmed a hamstring injury without any possibility to recover within next two weeks. Thus, the player departs to Russia where he will follow the rehabilitation course.
"The coaching and administrative staff of the Russian National team would like to wish Igor Denisov the fastest recovery."
Zenit's Artur Yusupov is expected to be named as Denisov's replacement in Russia's 23-man squad.
The news comes just two weeks after influential midfielder Alan Dzagoev was ruled out of the tournament after sustaining a broken metatarsal bone.
Russia begin their campaign against England on June 11 before facing Slovakia on June 15 and Wales five days later.