The pontiff expressed regret at the time for the way his speech was interpreted, and did not refer to it during his address at the Amman mosque.
Nonetheless, on Saturday the top religious adviser to Jordan's king mentioned the controversy.
"I would like to thank you for expressing regret over the lecture in 2006, which hurt the feelings of Muslims," Prince Ghazi bin Mohammed told the Pope.
"We realise that the visit [to Jordan] comes as a goodwill gesture and a sign of mutual respect between Muslims and Christians."
The BBC's David Willey, travelling with the Pope, says the pontiff is trying hard to show that the Catholic Church is anxious to foster greater respect, both for the beliefs the two faiths hold in common and for the areas where they differ.
But the Pope's efforts come amid misunderstandings and a lack of mutual comprehension, our correspondent says.
'Catalyst for tension'
During his address in Amman, the pontiff called on Jordan's Muslims and Christians to work together to improve their society.
BBC News, Amman
Pope Benedict has been treading an exceedingly careful path since his arrival here in order not to do or say anything in public likely to offend either his Muslim hosts or the Jewish authorities who will be his hosts in Jerusalem next week.
But even so, there has been some carping. Earlier in the day, the Pope talked of inseparable bonds between the Catholic Church and the Jewish people. Some clerics in Jordan reacted angrily.
Others remarked that the Pope had failed to remove his shoes when he visited the mosque in accordance with Muslim custom. All I can say is that I too was allowed to enter the mosque before the Pope's arrival without removing my shoes.
"Some assert that religion is necessarily a cause of division in our world and so they argue that the lesser attention given to religion in the public sphere the better," he said.
"Certainly, the contradiction of tensions and divisions between the followers of different religious traditions, sadly, cannot be denied.
"However, is it not also the case that often it is the ideological manipulation of religion, sometimes for political ends, that is the real catalyst for tension and division, and at times even violence in society?"
As he arrived in Amman on Friday he described himself as a "pilgrim of peace".
Jordan's King Abdullah welcomed the Pope to "the heartland of faiths for Christians and Muslims alike".
The 82-year-old Pope praised Jordan's "respect for religion".
The Pope's visit is aimed at encouraging the minority Christian community in the Middle East, and creating a better dialogue with Muslims and Jews.
As well as his 2006 speech to which some Muslims took offence, the Pope has also upset some Jews recently by rescinding the ex-communication of a Holocaust-denying bishop.
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