John had posted a picture of Putin on Instagram and thanked the Russian leader for "reaching out and speaking via telephone with me today".
A Kremlin spokesman, however, denied that Putin had made contact with the Rocket Man singer.
"Putin did not have a conversation with Elton John, and, what's more, we have not received any requests from him for a meeting," Dmitry Peskov was quoted as saying.
The 68-year-old music star said in an interview over the weekend that he would like to discuss Russia's attitude to gay rights with Putin.
"I'd say, come on. Gay people are not the problem here," the singer told BBC television.
In 2013, Putin signed off on a hugely controversial law banning the promotion or display of homosexuality in front of minors.
Elton John, who has two adopted children with his husband, the Canadian filmmaker David Furnish, said he hoped to use his influence to promote tolerance.
John performed in the then-Soviet Union in 1979 and still regularly plays shows in Russia.
But he used his 2014 show in St Petersburg to hit out at Russia's legislation.
"As a gay man, I've always felt so welcome here in Russia ... If I'm not honest about who I am, I couldn't write this music. It's not gay propaganda. It's how I express life. If we start punishing people for that, the world will lose its humanity," Sir Elton told the crowd.
- AFP