The statement comes as a surprise after the state environmental watchdog supported the plan of the state-owned pipeline company Transneft to run the pipeline less than a kilometer away from Baikal, the world's deepest lake.
Environmentalists have warned that an oil spill would leave the lake permanently damaged.
"If there is even the smallest, the tiniest chance of polluting Baikal, then we must think of future generations and we must do everything to make sure this danger is not just minimized, but eliminated," Putin said at a conference in the Siberian city of Tomsk, concluding that " the pipeline...must go above the northern border of Lake Baikal's watershed."
State television showed Putin pointing with a red pen at the projected route of the pipeline on a giant map, and saying it must be moved more than 40 kilometers further to the north.
(compiled from agency reports)