The day culminated with hundreds of Jews being herded into a barn and burned alive.
"This is why today, as a citizen and as the president of the Republic of Poland, I beg pardon. I beg pardon in my own name, and in the name of those Poles whose conscience is shattered by that crime," he said.
During the years of communism, the massacre in Jedwabne had always been blamed on the Nazis.
But in the last 12 months books have been published challenging that view - it is now believed that hundreds, possibly as many as 1,600 Jews, were murdered, not by the Germans, but by their own neighbours.
During the ceremony people placed stones, candles and wreaths on a new monument in memory of the victims.
New evidence
The inscription on the new memorial stone, written in Polish, Hebrew and Yiddish, reads: "To the memory of Jews from Jedwabne and the surrounding area, men, women and children, inhabitants of this land who were murdered and burnt alive on this spot on 10 July, 1941".
The fact that the inscription says nothing about who committed the massacre and makes no mention of any Polish involvement has caused bitterness among some Jews.
Evidence published in a book by Polish-American Jan Tomas Gross suggests that on 10 July 1941, the Poles of the village turned on their neighbours in a frenzy of bloodletting, which lasted eight hours.
The day culminated with hundreds of Jews being herded into a barn and burned alive.
The issue remains divisive - some locals, including the parish priest, stayed away from the ceremony in protest.
"These are all lies. I am spending the day quietly at home. It is Holocaust business. It is not my business. Germans are responsible, so why should we apologise?" the priest, Edward Orlowski, said.
Exhumations blocked
An official investigation has been hampered by Jewish laws forbidding the exhumation of the dead.
Investigators were allowed to analyse the top layer of corpses in one site only, whilst other mass graves remained untouched.
One of those who has returned for the ceremony is Ty Rogers from New York, whose grandfather was born in the village. He lost 26 relatives in one day.
Like many Jews, he is angry that for political reasons, the inscription on the new monument still will not apportion blame for the killings.
Jewish leaders say the book is forcing the Poles to re-work the view of themselves as victims and admit their own small part in the Holocaust.