Pope Benedict, under fire in Latin America for saying the Catholic Church had purified Indians, acknowledged on Wednesday that "unjustifiable crimes" were committed during the colonisation of the Americas.
But he stopped short of apologising as demanded by some leaders, including Venezuela's President Hugo Chavez.
"The memories of a glorious past cannot ignore the shadows that accompanied the process of evangelisation of the Latin American continent," the Pope said. "It is, in fact, not possible to forget the suffering, injustices inflicted by the colonisers against the indigenous population, whose human and fundamental rights have often been trampled," said the Pontiff, whose spoken message in Italian was stronger than a previously released text in English.
In a speech to bishops at the end of a visit to Brazil earlier this month, the Pope had said the Church had not imposed itself on the indigenous peoples of the Americas.
He had said they had welcomed the arrival of European priests at the time of the conquest as they were "silently longing" for Christianity. Embracing it purified them, the Pope had added.
Chavez has accused the Pope of ignoring the "holocaust" that followed Christopher Columbus's landing in the Americas in 1492. Indian leaders in Brazil have said they were offended by the Pope's "arrogant and disrespectful" comments.
Millions of tribal Indians are believed to have died as a result of European colonisation backed by the Church, through slaughter, disease or enslavement.
It was not the first time the German-born Pontiff's comments sparked controversy.
Benedict had infuriated Muslims worldwide in September 2006 with a lecture that seemed to depict Islam as an irrational religion tainted with violence.
He later expressed regret at the pain his comments caused and defused tensions during a trip to Turkey, where he prayed at a mosque and called Islam a peaceful faith.
The Pope, speaking on Wednesday to pilgrims gathered in St Peter's Square, noted that the crimes against Indians in the Americas were at the time already denounced by missionaries.
He also said remembering those crimes should not detract from the accomplishments of Christianity in Latin America. "Mentioning this must not prevent us from acknowledging with gratitude the marvellous work accomplished by the divine grace among these people in the course of these centuries," he said.