The organisation of the referendum was "nothing more than overconfidence and a superficial approach to solving fateful decisions for one's country, and Europe as a whole, on the part of the British leadership," Putin said,in comments broadcast on Russian state television.
"It will have consequences for the United Kingdom, for all of Europe and for us, of course," he added.
Many observers have said that Brexit would play into the Putin's hands as he has been accused of driving a wedge between EU members.
"Of course we closely followed what is happening but did not in any way influence the process and didn't even try to," the Russian strongman said.
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Kremlin spokesman Dmitry Peskov also stressed there was no indication that Moscow was pleased with the result of the vote.
"The topic of Brexit is Britain's domestic issue and an issue of its relations with the EU," said Kremlin spokesman Dmitry Peskov.
Prime Minister Dmitry Medvedev warned that Brexit's impact on markets has created "additional risks for the world economy, and therefore, for our economy."
The British vote to leave the EU demonstrated the desire to stop "feeding and subsidising weaker economies" and showed the population was "dissatisfied with the approach to security questions" amid the continent's migration crisis, Putin said.
Russia's foreign ministry said in a statement that the vote had "shown there are serious contradictions in the European Union."