"The EU commission fully rejects any false claims that attempt to distort the history of the Second World War or paint the victims like Poland as perpetrators," said EU commissioner Věra Jourová.
The EU Commission has supported Poland in a dispute with Russia over the history of World War II.
The dispute stemmed in part from comments Putin made in December stating that the Polish ambassador to Berlin had praised Adolf Hitler's plans to exterminate Jews.
"The EU commission fully rejects any false claims that attempt to distort the history of the Second World War or paint the victims like Poland as perpetrators," said the EU's commissioner for values and transparency, Věra Jourová.
Polish Prime Minister Mateusz Morawiecki said in December that the Russian president was lying about the war's history, emphasising that as time passes it's important to speak the truth.
"The memory about this evil is particularly important for Poland - the war's first victim," Morawiecki said in a statement.
Lithuania's Minister of Foreign Affairs Linas Linkevičius also backed Poland:
"We will not let the Kremlin manipulate history so easily and spread lies," Linkevičius said after meeting with his Polish counterpart. He said they would not allow Putin to "revive an image of Stalin as some sort of a good guy".
Manfred Weber, who leads the European People's Party said on Wednesday that the party would not accept "Putin's attempt to rewrite history".
"Every German politician has to assume the responsibility of our country. But every politician inside and outside of Europe also has the responsibility not to play with history," Weber told the EU's parliament during a debate.
"I cannot and we as EPP cannot accept Putin's attempt to rewrite history."
Putin has also criticised western powers for the 1938 Munich Agreement that allowed Hitler to annex Czechoslovakia, calling it an example of western powers' "collusion" with Hitler.
The Russian leader was lashing out after the European Parliament issued a resolution blaming World War II's outbreak in part on a nonaggression pact signed by Nazi Germany and the Soviet Union.
Poland was first invaded by Nazi Germany and two weeks later by Stalin's Soviet Union after the states signed the agreement.
Putin called the European Parliament's resolution "sheer nonsense".
The dispute comes ahead of the 75th anniversary of the Allied victory this spring.