Former US Secretary of State Hillary Clinton in March said Mr Putin's incursion into Crimea was akin to moves Hitler made in the years before World War Two, though she said the following day that she was not making a comparison.
Asked whether such comparisons to Hitler or Stalin went too far, Dalia Grybauskaite told German news magazine Focus on Sunday: "(Putin) uses nationality as a pretext to conquer territory with military means. That's exactly what Stalin and Hitler did. Such comparisons are spot on."
Ms Grybauskaite said Russia wanted to maintain its influence in territories that were once part of the Soviet Union and added it particularly wanted to keep the Baltic states dependent on it economically and in terms of energy policy.
She said Russia wanted the Baltic states - Latvia, Lithuania and Estonia - to become "unreliable members of Nato and EU".
"According to our information, there are Russian offers in other Baltic states to reduce the prices for oil or gas if these countries leave Nato," she said.
Ms Grybauskaite said the West should seek to become economically independent of Russia and diversify, because it was "too risky" for countries to continue to depend on Russia.
"Putin has a missionary vision to defend the eastern hemisphere. He has in mind a Russia like that of the time of Catherine the Great," she said.
The West has accused Russia of supporting the insurgency in Russian-speaking eastern Ukraine that followed Moscow's annexation of Crimea.
She said Russia and Putin were "characterised by aggressiveness, violence, and a willingness to overstep boundaries" and added that Baltic states and Poland "constantly" experienced this, with military exercises taking place almost every week in Kaliningrad, Russia's western enclave.
She said a Russian invasion of the Baltic states was unlikely given their Nato membership, but added they needed to be better prepared.