In Istanbul, Vatican officials said the remark shows the need for faiths to fight "violence in the name of God."
The trip is Benedict's first visit to an Islamic country as pontiff, seeking dialogue with Muslims who were angered over a speech he made in September in which he cited a medieval text that linked Islam and violence.
Al Qaeda in Iraq issued its statement on an Islamic militant Web site it often uses to post messages.
"The pope's visit, in fact, is to consolidate the crusader campaign against the lands of Islam after the failure of the crusader leaders ... and an attempt to extinguish the burning ember of Islam inside our Turkish brothers," it said.
Vatican spokesman Rev. Federico Lombardi said "neither the pope nor his entourage are worried" by the statement.
"This type of message shows once again the urgency and importance of a common commitment of all forces against violence," Lombardi said. "It also shows the need of various faiths to say 'no' to violence in the name of God."
Earlier on Wednesday, the pope held a Mass at one of the holiest Christian places in Turkey as part of his efforts to reach out to the Roman Catholic minority in the mostly Muslim country.
The pontiff conducted the open-air Mass next to the ruins of a house where the Virgin Mary is thought to have spent her last years.
Security forces had sealed off the area and only 250 invited guests attended, making it one of the smallest crowds to attend a papal Mass.
The Vatican said the site could accommodate up to 2,000 people. Many of those attending held small Turkish and Vatican flags. In bright sunshine, the pope stood on a dais under a white, flower-covered canopy.
A paramilitary helicopter hovered low over the crowd as the pope arrived, and registered guests went through three separate metal detectors before reaching the sacred site.
A military policeman said security details weren't given out to officers until the last minute, apparently to keep the pope's exact route secret.
The ruins of the house, whose earliest foundations date to the first century, have become a popular place of pilgrimage since the 1950s. A chapel was built over the ruins, and some believe in the healing powers of both the chapel and waters flowing from a nearby spring. The site is nestled on a wooded mountain between the ancient city of Ephesus and the town of Selcuk, near the Aegean coast.
Of Turkey's 70 million people, some 65,000 are Armenian Orthodox Christians, 20,000 are Roman Catholic, and 3,500 are Protestant, mostly converts from Islam. Another 2,000 are Greek Orthodox and 23,000 are Jewish. The Christian minority has complained of discrimination and persecution by the Muslim majority.
On Tuesday, the first day of his trip to Turkey, Benedict urged religious leaders of all faiths to "utterly refuse" to support any form of violence in the name of faith. Turkey's top Muslim cleric complained to the pontiff of a growing "Islamophobia" in the world.
Benedict sought a careful balance as he held out a hand of friendship and "brotherhood" to Muslims, hoping to end the outcry from many Muslims over the pontiff's recent remarks linking Islam to violence. It is his first trip to a Muslim country.
In a gesture welcomed by his hosts as well as the Muslim world at large, he expressed support for Turkey's efforts to join the European Union, moving away from opposition he voiced when he was a cardinal.
The pope planned to travel later Wednesday to Istanbul to meet Bartholomew I, leader of the world's 300 million Orthodox Christians. The two major branches of Christianity represented by Bartholomew and Benedict split in 1054 over differences in opinion on the power of the papacy, and the two spiritual heads will meet in an attempt to breach the divide and reunite the churches.