Foreign ministry spokeswoman Maria Zakharova wrote on Facebook that the hacker targeted "an old site that has not been used for a long time," adding that "specialists are working out what happened."
The attack came after Washington earlier this week formally accused the Russian government of trying to "interfere" in the 2016 White House race by hacking, charges the Kremlin has repeatedly dismissed.
"If they establish there was hacking by Americans, even of a resource that wasn't working, this is far from pleasant," Zakharova wrote.
Alternatively, the latest hack simply shows that the "US elections have wound up people to such a state that they start smashing everything," Zakharova wrote.
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The foreign ministry's main website was apparently working normally on Sunday afternoon.
On Saturday, a hacker who calls himself the Jester tweeted: "I'm Jester & I approve this message via the Russian Foreign Affairs Website."
"Comrades! We interrupt regular scheduled Russian Foreign Affairs Website programming to bring you the following important message," he wrote.
"Knock it off. You may be able to push around nations around you, but this is America. Nobody is impressed," he added.
CNN reported that the jester's attack overnight Moscow time included the piercing sound used for civil alert messages about extreme weather.
The hacker said he was writing on the ministry site to complain after waves of distributed denial of service (DDoS) attacks pounded Twitter, Netflix and other major websites on Friday, accusing Russia of being behind this.
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