Pope Benedict XVI called on each community to overcome past prejudices
Pope Benedict XVI has called for mutual respect between Christians and Muslims to heal tension between the two faiths.
The first forum between Muslim and Catholic officials at the Vatican aim to defuse tensions between the world's two biggest faiths.
The Pope said "each individual's... freedom of religion" must be safeguarded, stressing that religious persecution was "unacceptable".
There was outrage in 2006 when the Pope linked Muslims to violence in the past.
He apologised for those remarks, saying he was quoting a medieval scholar and never meant to make a direct connection.
But it triggered violent protests and prompted leading Muslim scholars to launch an appeal to the Pope for greater theological dialogue, called the Common Word.
That manifesto now has more than 250 signatories.
In remarks on the third and final day of the conference at the Vatican, Pope Benedict said: "Political and religious leaders have the duty of ensuring... each individual's freedom of conscience and freedom of religion."
Muslims and Christians have different approaches in matters concerning God... but must consider themselves members of one family
Pope Benedict XVI
"My hope... is that these fundamental human rights will be protected for all people everywhere.
"The discrimination and violence which even today religious people experience throughout the world, and the often violent persecutions to which they are subject, represent unacceptable and unjustifiable acts."
The Pope said that such persecutions were "all the more grave and deplorable when they are carried in the name of God".
The Vatican has protested against attacks on Christians in Iraq and Saudi Arabia's ban on their worshipping in public.
"Muslims and Christians have different approaches in matters concerning God", the Pope said, "but must consider themselves members of one family".
Some of the Muslim speakers pointed out that Muslims had been the focus of persecution too.
Mustafa Ceric, the mufti of Bosnia, said: "My brothers, Bosnian Muslims, suffered genocide" during the Balkan wars of the 1990s.
The Pope has sought to improve ties with the Muslim world since 2006
Seyyed Hossein Nasr of Iran, who teaches Islamic studies in Washington, said that both Muslims and Christians "believe in religious freedom".
However, he added: "We, Muslims, do not allow an aggressive proselytising in our midst that would destroy our faith in the name of freedom, any more than would Christians if they were in our situation."
The talks are being attended by 29 Christian and 29 Muslim scholars.
A joint final declaration is expected later on Thursday.
There are about two billion Christians in the world, just over half of them Catholics.
Muslims, who now number about 1.3 billion, recently overtook the number of Catholics worldwide for the first time.