Sergey Andreev said today he had no intention of offending the Polish nation and added: "I regret that I wasn't sufficiently precise."
He spoke to reporters after being summoned to the Foreign Ministry following comments in a TV interview Friday that sparked the uproar.
World War II began after Nazi Germany and the Soviet Union sealed a secret pact in 1939 to divide up Poland and other parts of Eastern Europe. Millions of Polish citizens died in the conflict.
"Polish policy led to the disaster in September 1939, because during the 1930s Poland repeatedly blocked the formation of a coalition against Hitler's Germany. Poland was therefore partly responsible for the disaster which then took place," Andreev said.
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Poland's Foreign Ministry issued a statement of strong protest on Saturday, accusing Andreev of undermining historical truth, and summoned him for a meeting Monday with a director of the ministry's department on Eastern affairs.
"During the conversation it was noted that these statements are untrue and contrary to the findings of Polish and Russian historians," Foreign Ministry spokesman Marcin Wojciechowski said in a statement.
Ties between the two Slavic neighbors have never been easy since Poland rejected Soviet-backed communism in 1989 and embraced the West. Relations have faced new strains since Russia annexed Crimea, an action Poland has strongly condemned.
In his interview on Friday Andreev said relations are the worst they have been since 1945, and on Monday he said he sticks by that opinion.
In other incidents that have caused tensions, the graves of Soviet soldiers in Poland were recently vandalized while a Polish town dismantled a monument to a Soviet World War II general. Moscow has protested both incidents.