Pakistan's parliament unanimously condemned the pope, and the Foreign Ministry summoned the Vatican's ambassador to express regret over the remarks.
Benedict quoted from a book recounting a conversation between 14th-century Byzantine Christian Emperor Manuel Paleologos II and a Persian scholar on the truths of Christianity and Islam.
"The emperor comes to speak about the issue of jihad, holy war," the pope said. "He said, I quote, 'Show me just what Muhammad brought that was new, and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached."'
The Vatican said the pope did not intend the remarks — made in Germany on Tuesday during an address at a university — to be offensive.
Benedict did not explicitly agree with the statement; nor did he repudiate it.
A Vatican official urged Islamic scholars to re-read the pope's address. Monsignor Felix Machado, who works to improve inter-religious dialogue, said it is clear the pope's address cannot be considered an attack on Islam, but rather an effort at dialogue because Benedict stressed the value of humanity's religious cultures and among them gave an important place to Islam, reports CBS News correspondent Sabina Castelfranco from Rome.
The comments raised tensions ahead of his planned visit to Turkey in November — his first pilgrimage to a Muslim country.
Salih Kapusuz, a deputy leader of Turkish Prime Minister Recep Tayyip Erdogan's party, said Benedict's remarks were either "the result of pitiful ignorance" about Islam and its prophet, or a deliberate distortion.
"He has a dark mentality that comes from the darkness of the Middle Ages. He is a poor thing that has not benefited from the spirit of reform in the Christian world," Kapusuz was quoted as saying by the state-owned Anatolia news agency. "It looks like an effort to revive the mentality of the Crusades."
"Benedict, the author of such unfortunate and insolent remarks, is going down in history for his words," he said. "He is going down in history in the same category as leaders such as (Adolf) Hitler and (Benito) Mussolini."
Turkey's staunchly secular opposition party also demanded that Benedict apologize to Muslims before his visit.
"The pope has thrown gasoline onto the fire ... in a world where the risk of a clash between religions is high," said Haluk Koc, deputy head of the Republican People's Party, as a small group of protesters left a black wreath in front of the Vatican's embassy in Ankara.
Lebanon's most senior Shiite Muslim cleric denounced the remarks and demanded the pope personally apologize.
"We do not accept the apology through Vatican channels ... and ask him (Benedict) to offer a personal apology — not through his officials — to Muslims for this false reading (of Islam)," Grand Ayatollah Mohammed Hussein Fadlallah told worshippers.