Putin, dressed in a puffy white suit, made three brief flights over the arctic Yamal Peninsula on Wednesday as part of the "Flight of Hope" project to boost Siberian crane populations.
A video of the flights posted on YouTube by TV channel RT shows Putin soaring through the air, his suit billowing in the wind, followed by several birds.
The flights were supposed to show the birds, which were raised in captivity, the route to specially created wintering grounds in southern Uzbekistan, the Kremlin said in a statement Thursday.
The trip to their traditional wintering grounds in India has become too hazardous due to poaching in Afghanistan and Pakistan, the statement said.
Putin's flight was not his first publicized encounter with animals.
In 2008, he visited the Ussuriisky Nature Reserve, where he shot a tigress with a tranquilizer gun and tagged her with a GPS collar.
The event caused a scandal when environmentalist Dmitry Molodsov wrote in March 2012 that the tigress was tranquilized before Putin's visit and later died as a result of a sedative overdose.
Putin has also taken part in projects to preserve white whales, snow leopards and Amur leopards.
He's also been photographed horseback riding in southern Siberia, fishing ancient pottery out of the Black Sea, and swimming in a Siberian lake.