The protest had been organised by pro-Islamic political party Felicity, whose leaders have said they were offended by the pope's comments.
The pope's visit is widely seen as an opportunity to improve relations with Muslims
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The party also draped banners over welcome signs along the route from Istanbul's airport reading: "No to an alliance of crusaders, let the pope not come."
Police said they were preparing for up to 15,000 people to attend the demonstration, the largest anti-pope protest to date.
Such protests have to be approved by the Turkish police, though spontaneous gatherings are not uncommon.
The pope said at the Vatican on Sunday: "Starting right now, I want to send a cordial greeting to the dear Turkish people, rich in history and culture."
A visit to Istanbul's Sultanahmet, or Blue Mosque, has been added to the pope's itinerary, a move seen as a further attempt at reconciliation with the Muslim world.
The pope has previously spoken out against Turkey's bid to join the EU, and has called for a return to fundamental Christian values in Europe.
His trip to Turkey will be his first official visit as pope to a predominantly Muslim country.
Turkey's ruling AK party has kept a low profile in preparations for this visit, with talks still in progress as to whether Tayyip Erdogan, Turkey’s prime minister, will meet the pope.
With a general election due next year the AK party, which has roots in political Islam, must balance a rise in nationalism with their support base among conservative Muslims.
Benedict is scheduled to stay for four days and will meet the Istanbul-based leader of the world's 300 million Orthodox Christians, Patriarch Bartholomew I.