Clinton, a potential 2016 presidential contender, warned during her a speech at the University of California, Los Angeles, that "all parties should avoid steps that could be misinterpreted or lead to miscalculation at this delicate time."
Putin has said he was protecting ethnic Russians by moving troops into Crimea.
Clinton said Tuesday at a closed fundraising luncheon in Long Beach that Putin's actions are similar what happened in the Nazi era in Czechoslovakia and Romania.
"Now if this sounds familiar, it's what Hitler did back in the '30s," Clinton said, according to the Press-Telegram of Long Beach. "Hitler kept saying, 'They're not being treated right. I must go and protect my people.' And that's what's gotten everybody so nervous."
Responding to a question submitted at the UCLA talk, Clinton said she was not making a comparison although Russia's actions were "reminiscent" of claims Germany made in the 1930s, when the Nazis said they needed to protect German minorities in Poland and elsewhere in Europe.
"The claims by President Putin and other Russians that they had to go into Crimea and maybe further into eastern Ukraine because they had to protect the Russian minorities, that is reminiscent of claims that were made back in the 1930s when Germany under the Nazis kept talking about how they had to protect German minorities in Poland and Czechoslovakia and elsewhere throughout Europe," she said.
"I just want everybody to have a little historic perspective. I am not making a comparison, certainly. But I am recommending that we perhaps can learn from this tactic that has been used before," she said.
Clinton said Putin is trying to "re-Sovietize" the periphery of Russia but is actually squandering the potential of his nation and "threatening instability and even the peace of Europe."
In recent days, some Republicans, including Sen. John McCain, R-Ariz., have criticized the Obama administration's policy in Ukraine. Clinton echoed President Barack Obama's assessment that Russia's intervention was a violation of international law, and she said she supported the administration's call for Russia "to refrain from the threat or use of force."
Kathryn Stoner, a Russia expert at Stanford University's Freeman Spogli Institute for International Studies, said she considered Clinton's comparison between Putin and the tactics of Nazi-era Germany "a bit of a stretch," in part because Putin "doesn't look like he is intent on spreading across the Ukraine and permanently occupying this area."
In a delicate diplomatic situation "I don't think it's helpful on either side to say things like this, but in these crises it happens," Stoner added.