In November, the singer said he had talked to the Russian President on the phone and was arranging to meet him to discuss his concerns over gay rights in the country.
But a Kremlin spokesman has now said that will not happen as there was "no appropriate time in the two men's schedules".
However Dmitry Peskov said that they could still meet at a later date.
"We were in correspondence with him (Elton John) a couple of weeks ago, because there had been an agreement that, if their schedules allow, this meeting would take place. President Putin expressed readiness for this meeting. But this time, the meeting won't take place, unfortunately," he told reporters.
"Their schedules do not match up. But this does not mean that such a meeting won't take place next time."
Sir Elton will be performing at the Ice Palace in St Petersburg on 28 May, and on 30 May in Moscow at Crocus City Hall, as part of his world tour.
Last September, the singer fell victim to prank callers pretending to be the Russian leader.
Vladimir Krasnov and Alexei Stolyarov phoned the singer, after Sir Elton told BBC News he wanted to meet Mr Putin to discuss gay rights in Russia - describing the president's attitude to gay people as "isolating and prejudiced".
The hoax phone call was aired on Russian TV.
However the singer later received a genuine call from the president.
He told the BBC's Today programme: "He was very affable, he was very apologetic, he was very sincere.
"As soon as I can get a date in my diary that coincides with him, then I will be going... to Moscow and I will meet him."
Sir Elton John will not meet Vladimir Putin when he visits Russia this month.