"Unfortunately this time it won't work out," Putin's spokesman Dmitry Peskov told journalists, asked if Putin would manage to meet the star when he gives a concert in Moscow on Monday.
"The schedules don't fit," Peskov said. "That doesn't mean such a meeting won't happen next time."
Peskov said he "had been corresponding a couple of weeks ago" with the musician over a possible meeting.
"As you know, there was indeed an agreement that if their schedules fitted, there would be a meeting, President Putin expressed readiness to do this," Peskov said.
The British music legend, who is gay and is a prominent fundraiser for AIDS charities, said in September last year that he wanted to talk about gay rights with Putin.
"I'd love to meet him," he told the BBC, saying he would tell the Russian leader: "Don't isolate and be prejudiced against gay people."
Putin in 2013 signed a hugely controversial anti-gay law banning the promotion or display of homosexuality to minors.
Putin then responded with a genuine call, saying he was ready to meet for a discussion, but since then nothing more has been said of this.
Monday's concert, when John may voice his views on gay rights in Russia, comes as Moscow city authorities has banned a gay pride event planned for Friday and Saturday, the sixth such ban under current mayor Sergei Sobyanin.
