In a pre-Christmas holiday press conference, Obama said he told Putin to "cut it out" during a face-to-face encounter in China where a G20 meeting was being held.
Obama added that after warning Putin, there was no further evidence of Russian tampering. Russia has denied U.S. accusations of cyberattacks against U.S. political figures and institutions ahead of the presidential and congressional elections.
Two senior government officials told Reuters that the FBI backs the CIA's view that Russia intervened to help Republican Donald Trump win the presidential election.
Obama left open the door to U.S. retaliation against Russia to discourage it and other nations from further computer hacking.
The president also said that he hoped that Trump, who takes office on Jan. 20, should be similarly concerned about Russia's actions and that the investigation should not become "a political football" between Republicans and Democrats.
Trump has maintained that he won the election fairly and has bristled at suggestions that Moscow influenced the outcome.
But Democrats have repeatedly noted that Trump during his campaign has spoken glowingly about Putin and since winning the election has picked top aides in the incoming administration with ties to Russia.
At one point during the heated presidential campaign, Trump publicly encouraged Russia to hack Democratic rival Hillary Clinton's emails.