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Beginning a delicate four-day trip under heavy security to the predominantly Muslim country, Benedict quickly set to work trying to soothe still simmering rows.
Speaking to reporters on his plane, Benedict said a main purpose of his trip was to foster peace and better understanding between Christians and Muslims.
Addressing Turkey's President Ahmet Necdet Sezer later, he expressed his "particular esteem" for Muslims and said he wanted to promote "dialogue as a sincere exchange between friends".
Benedict's comments on the first day of his trip appeared to go a long way towards making up for a speech in Germany in September where he quoted a Byzantine emperor who said Islam was violent and irrational. The speech infuriated Muslims worldwide.
In a public address to the Pope, Turkey's Religious Affairs Director, Ali Bardakoglu, made it clear that all may have been forgiven but perhaps not forgotten.
Bardakoglu spoke out against growing "Islamophobia, which expresses the mentality that the religion of Islam is containing and encouraging violence".
In his speech, Benedict said Christians and Muslims must continue an open dialogue because they believe in the same God and agree on the meaning and purpose of life.
The atmosphere seemed cool at the meeting between Benedict and Bardakoglu but Vatican spokesman Father Federico Lombardi said the Muslim cleric's speech was "thorough, positive and respectful, never polemical".
Earlier, Prime Minister Tayyip Erdogan told reporters that in a private meeting at the airport, Benedict had told him he backed Turkey's bid to join the European Union.
"He said 'we are not political but we wish for Turkey to join the EU'," Erdogan told journalists.
Erdogan, who began his career in Islamic politics, added: "The most important message the Pope gave was towards Islam, he reiterated his view of Islam as peaceful and affectionate."
Asked to explain the Vatican's precise position, spokesman Father Lombardi said it could not take any political stand but "encourages and views positively Turkey's path of dialogue, rapprochement and participation in Europe based on common values and principles".
Erdogan appeared to have no doubts that Benedict had changed his stand from 2004, when he told a French newspaper before he was elected Pope that Turkey would be "in permanent contrast to Europe" if it joined.
Erdogan, who had originally said he was too busy to meet the Pope, instead greeted him warmly at the airport before leaving for the NATO summit in Latvia.
Fears of large protests by Islamists and nationalists failed to materialise, with only two small and peaceful demonstrations reported in Ankara. About 3,000 police were out on patrol to keep order, with snipers on buildings near papal events.
Instead of protesters' shouts, Benedict could hear muezzins calling Muslims to prayer both as he laid a wreath at the mausoleum of the republic's founder Mustafa Kemal Ataturk.
The visit by the leader of 1.1 billion Roman Catholics was meant to be a mostly Christian event but it has taken on wider ramifications in Western-Islamic relations, Catholic-Muslim relations and Turkey's own desire to be part of Europe.
More than 20,000 Muslim protesters rallied against the Pope's trip on Sunday in Istanbul, chanting "Pope don't come."
The main focus of his trip will be talks on Christian unity with Patriarch Bartholomew, the Istanbul-based spiritual head of the world's 250 million Orthodox Christians. Reuters