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A government spokeswoman confirmed to Reuters that Prime Minister Mateusz Morawiecki would not attend the summit and would send Foreign Minister Jacek Czaputowicz instead.
Morawiecki informed Israeli Prime Minister Benjamin Netanyahu of his decision to cancel his visit in a telephone call on Sunday afternoon, spokeswoman Joanna Kopcinska said.
The summit of four central and Eastern European countries is set to be held in Jerusalem this week.
Poland's government has sought to debunk references to potential Polish collaboration in the Holocaust, in an effort to "fight for the truth," Morawiecki told Poland's parliament last year.
Netanyahu's office said in a statement the prime minister, who was in Warsaw for a U.S.-sponsored Middle East conference when he made the comments, had been misquoted by The Jerusalem Post, which issued a corrected story.
In a later statement, Netanyahu's office said in his remarks on the question of Polish collaboration with Nazi occupiers, he had not cast any blanket blame.
Netanyahu's acting foreign minister, Israel Katz, sounded circumspect about Morawiecki's cancellation.
"In diplomacy one always tries to avoid causing offence. But no one will change historical truth," Katz told Israel's Reshet 13 TV. "Poles collaborated with the Nazis, certainly."
Israeli Ambassador Anna Azari was summoned by Poland's government on Friday and was asked to clarify Netanyahu's comments.
Morawiecki said in an interview published on Sunday by Polish news agency PAP that Azari explained that Netanyahu was referring to individual cases of Poles collaborating with Nazis.
Poland had summoned Israeli Ambassador Anna Azari on Friday for clarification of Netanyahu's comments.
Tensions between Israel and Poland ran high last year after Poland introduced new legislation that would make the use of phrases such as "Polish death camps" punishable by up to three years in prison.
After pressure from the U.S. government and an outcry in Israel, Poland watered down the legislation, removing the prison sentences.
Many Poles still refuse to accept research showing thousands participated in the Holocaust in addition to the thousands who risked their lives to help the Jews.