Benedict's remarks to Italian-speaking pilgrims at his general audience in the square were even stronger than the comments in English.
"It is not possible, indeed, to forget the sufferings and injustices inflicted by colonizers on the indigenous populations, whose fundamental human rights were often trampled on," Benedict said.
The pontiff said he was making a "dutiful mention of such unjustifiable crimes" and said some missionaries and theologians in the past had condemned them.
Pope recognizes colonial injustices
Indigenous rights groups, plus the presidents of Venezuela and Bolivia, were incensed.
The episode is the latest in which the pope, elucidating a theological point he firmly believes, made statements that appeared to ignore or disregard cultural and historical sensitivities.
The most explosive example occurred last year when, during a speech on faith and reason in Germany, he quoted comments by a Byzantine emperor widely seen as insulting to Islam. The speech triggered rage across the Muslim world, prompting the pope to make several subsequent statements, not apologizing for what he said but saying he was sorry for the reaction his words had caused.