Mr Netanyahu said Mateusz Morawiecki’s comments were “outrageous” and demonstrated an “inability to understand history”.
It comes after Poland passed a law criminalising and implementing prison terms for statements which suggest Poland bears responsibility for crimes committed by Nazi Germany.
Under the bill, which is an amendment to an existing law, the use of phrases such as “Polish death camps” can be punished by up to three years in prison or a fine.
Mr Morawiecki, head of the ruling conservative Law and Justice Party, was asked by an Israeli journalist at the Munich Security Conference in Germany whether anyone who said there were Polish collaborators in the Holocaust would be deemed a criminal in Poland with the new law in place.
Mr Morawiecki said: "It's extremely important to first understand that, of course, it's not going to be punishable, not going to be seen as criminal to say that there were Polish perpetrators – as there were Jewish perpetrators, as there were Russian perpetrators, as there were Ukrainian... not only German perpetrators."
Nr Netanyahu, who is also attending the Munich conference, rapidly hit back.
He said: “The Polish Prime Minister’s remarks here in Munich are outrageous. There is a problem here of an inability to understand history and a lack of sensitivity to the tragedy of our people.”
He added: “I intend to speak with him forthwith.”
The stern statement comes after Israel, home to the largest community of Holocaust survivors in the world, criticised Poland for plans to outlaw statements describing Nazi death camps as Polish.
At the end of January, Mr Netanyahu said Israel had “no tolerance for the distortion of truth, the rewriting of history and the denial of the Holocaust”.
The Israeli Foreign Ministry also voiced concern over the timing of the bill which passed the lower house on the eve of International Holocaust Remembrance Day.
Poles have long objected to phrases such as “Polish death camps” which imply Poland was partially responsible for camps like Auschwitz.
The death camps were built and operated by German Nazis after they invaded Poland in 1939. However historical accounts show some Poles collaborated with the Nazis and committed heinous crimes against the Jews during the Second World War.
Research published in the wake of the fall of communism in 1989 demonstrated thousands of Poles killed Jews or denounced those who concealed them to the Nazi occupier.
Around three million Jews who lived in pre-war Poland were murdered by the Nazis - constituting about half of all Jews killed in the Holocaust.
The new Polish law, which has also been condemned by global Jewish organisations, states that "whoever accuses, publicly and against the facts, the Polish nation, or the Polish state, of being responsible or complicit in the Nazi crimes committed by the Third German Reich… shall be subject to a fine or a penalty of imprisonment of up to three years".
However, it includes the qualification that a person "is not committing a crime if he or she commits such an act as part of artistic or scientific activities".
Critics of Poland’s new law argue it will restrict historical debate and freedom of expression in the country.
Poland’s ruling Law and Justice Party (PiS) is facing accusations of rousing nationalistic sentiment to boost the far right. Since the collapse of communist rule, the country has been a surge in nationalist activity and the far right has become increasingly emboldened.
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