The visit, his first to a Muslim-majority nation, is seen as an attempt to reconcile and bridge the growing divide between the two faiths.
"The scope of this visit is dialogue, brotherhood, a commitment for understanding between cultures, between religions, for reconciliation," he told told reporters aboard his aircraft en-route to Ankara.
He was received at Ankara airport by Prime Minister Recep Tayyip Erdogan, who later quoted the Catholic leader as saying that '"We at the Vatican are not politicians, but we are in favour of Turkey's path toward joining the European Union."
Before he was appointed Pope in April last year, Cardinal Joseph Ratzinger had expressed reservations over this, telling a French newspaper that Turkey's Islamic values were incompatible with a Christian continent.
After a brief meeting with Erdogan at the airport, the Pope visited the mausoleum of Mustafa Kemal Atatürk, the founder of modern Turkey and then met briefly with President Ahmet Necdet Sezer.
He then visited Ali Bardakoðlu, the head of Turkey's Religious Affairs Directorate, in his office, and the two addressed a joint meeting.
In his speech, the Pope called for an open dialogue between Christians and Muslims, saying they agreed on the meaning and purpose of life. But was dampened by Bardakoglu's response. Warning against growing 'Islamophobia, which expresses the mentality that the religion of Islam is containing and encouraging violence,' Bardakoglu said: 'The so-called conviction that the sword is used to expand Islam in the world is causing Islamophobia.'
The Pope left Ankara for Istanbul on Wednesday. He is also expected to visit the Haghia Sophia, a Byzantine Christian church that was turned into a mosque during the Muslim conquest in 1453 and is now a museum. In 1967, Pope Paul VI had created an uproar among Turkey's secular leaders by dropping to his knees in prayer while visiting the museum.
Image: Pope Benedict XVI (front) speaks at the Directorate of Religious Affairs in Ankara as Ali Bardakoglu, secular Turkey's top religious official, looks on.
Photograph: Vincenzo Pinto/AFP/Getty Images
Also see: Pope Benedict XVI: 6 Questions