Putin's comments came in his final address to Parliament before his inauguration as president in May, RIA Novosti reported.
"NATO is a Cold War-era relic," Putin, the current prime minister, told State Duma lawmakers. "It was created in times of a bi-polar system of international relations.
"But today's situation is different and it's not clear what an organization like NATO is for."
But Putin cited NATO's role in stabilizing international affairs and pointed to its work in Afghanistan.
"NATO acts within the U.N. mandate in Afghanistan … and it is in our national interests, too, to have the Afghan situation brought under control," he said.
Russia has allowed NATO cargo to Afghanistan to cross its territory since 2009 and last year agreed to allow cargo to come through Russia in the opposite direction as the alliance prepares to withdraw troops from Afghanistan.