The 68-year-old singer, who wants to talk to Putin about his "ridiculous" attitude to gay rights, previously fell victim to pranksters who impersonated the Russian leader on the phone, reported BBC online.
But Kremlin spokesman Dmitry Peskov told Russian media that Putin had this time called the singer and asked him not to be offended by the hoax.
Putin said he was ready to meet John - when their schedules allowed it - and discuss "any issues of interest" to the British star, Peskov said.