Polish President Lech Kaczynski has said there is no place in his country for anti-Semitism.
A monument to the victims was unveiled at the ceremony
His comments came at a ceremony to mark the 60th anniversary of an anti-Semitic massacre in which 42 people, mostly Jews, were killed by Poles in Kielce.
In a statement read out on his behalf, Mr Kaczynski said what had happened in Kielce was a crime.
His remarks come as Poland faces new allegations by the EU that racism and homophobia are on the rise.
During World War II, 90% of Poland's 3.5m Jews were murdered by the Nazis in the Holocaust.
But the Kielce pogrom was particularly shocking because it took place just over a year after the end of the war.
It was one of the blackest pages in Polish history, the BBC's Adam Easton in Warsaw says.
After rumours spread that a young Polish boy had been kidnapped by a Jewish family, some of the city's residents and the police killed an estimated 40 Jews.
The violence caused many of Poland's 250,000 Jews who survived the Holocaust to emigrate.
In a speech read out in the president's absence due to illness, Mr Kaczynski said, "As the president of Poland, I want to say it loud and clear: what happened in Kielce 60 years ago was a crime.
"This is a great shame and tragedy for the Poles and the Jews, so few of whom survived Hitler's Holocaust."
The recent entry of the far-right League of Polish Families party into the conservative coalition government has raised concerns about anti-Semitism in Poland.
"There is anti-Semitism in Poland today. It, however, still does not play a significant role in society, in large measure thanks to the teachings of John Paul II," Poland's chief rabbi Michael Schudrich told the BBC.
"The level of anti-Semitism here is actually far less than in almost any other European country today," he said.
At the ceremony on Tuesday, a white monument in the shape of the number 7 was also unveiled, a reminder that the killings took place at 7 Planty Street in the seventh month of the year.