Roscosmos spokesman Alexei Kuznetsov on Sunday confirmed the hospitalization but would not elaborate.
Russian news agencies earlier quoted Roscosmos press office as saying that Popovkin had been taken to hospital with "physical and emotional exhaustion."
The 54-year-old Popovkin had been leading the Russian space agency since April.
Russian tabloid Life News on Sunday posted a photo of Popovkin with his head bandaged, and quoted sources as saying that the space chief had been drunk when taken to hospital.
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