Pope Benedict XVI tried on Wednesday to placate the anger expressed by Latin American Indians this month after he said that they had been purified by the Catholic Church.
Speaking at his general audience in St Peter's Square, the pontiff said no one could ignore the "suffering and the injustices inflicted by the colonisers of the indigenous peoples" of the Americas.
He said that, despite the "glorious" progress of the Christian faith in Latin America after its discovery in 1492, there were also "shadows" in the evangelising work.
The rights of native peoples were often "trampled on," he said.
In a speech to Latin American bishops at the end of his May 9-14 visit to Brazil, Benedict offended many Indians in North and South America by saying the Church had not imposed itself on their ancestors.
He said the tribal Indians of the time welcomed European priests because they were "silently longing" for Christianity.
Millions of Indians are thought to have been slaughtered, killed by disease or enslaved as a result of colonisation by European powers who were supported and accompanied by the Roman Catholic Church.
After the pope's May 13 speech, angry Indian leaders in Brazil said they were offended by the pontiff's "arrogant" comments.
Venezuelan President Hugo Chavez proposed last weekend that Benedict apologise to the first peoples of America for saying that Christianity had spread naturally through the continent.
"How can the pope say the evangelisation wasn't an imposition?" he said. "Why did the indigenous people have to flee to the forests and the mountains?"
In actual fact, the Church has long recognised the atrocities that took place at the time and Pope John Paul asked forgiveness for the role Christians played in slavery in America and elsewhere.
As early as the 16th century, a Spanish priest called Bartolomé de Las Casas denounced in a book the brutal treatment of Latin American natives by the Spanish conquistadores.
American and Spanish bishops have begun procedures they hope will lead to the canonisation of the priest, who was the first bishop of Chiapas, Mexico.
He was forced to resign from his seat in the New World precisely because of his stance.
