"Putin... Had a talk with Elton John," his spokesman Dmitry Peskov said, quoted by RIA Novosti state news agency.
The Russian leader told the British singer not to get offended at the pranksters who called him last week pretending to be Putin and his spokesman, Peskov said.
"Putin called and said 'I know that some guys played a phone prank on you. Don't get offended at them, they're harmless, but of course that doesn't excuse them,'" Peskov said.
Putin suggested a meeting with the pop legend to discuss any topic, Peskov said, while not specifically referring to gay rights, which Elton John has said he wants to debate with the Russian strongman.
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"Putin said he knows what a popular performer Elton John is and if their schedules match in the future, he is ready to meet and discuss any questions that interest him," Peskov said.
John last week said he had received a phone call from Putin after saying he wanted to meet the president to discuss Russia's failure to respect gay rights.
John responded to the revelation that the call was a hoax by saying that "Pranks are funny. Homophobia, however, is never funny."
In 2013, Putin signed off on a hugely controversial law banning the promotion or display of homosexuality in front of minors.
John, who is gay, has raised more than USD 321 million through his foundation for AIDS treatment and prevention.