About 2,000 Palestinians protestors marched in the Gaza Strip on Friday waving the green flags of Hamas and chanting praises to "God and his prophet".
Palestinian prime minister Ismail Haniya criticised the pope's comments, saying: "These remarks go against the truth and touch the heart of our faith.
"The pope should revise his comments and stop attacking Islam, which is the religion of more than 1.5 billion people."
Aljazeera's correspondent in the Palestinian territories reported that two churches in the West Bank city of Nablus were hit by firebombs early on Saturday.
The bombs targeted a Roman Catholic church that was under construction, and an Anglican church, causing minor damage to the outside walls and windows of the two churches.
In Gaza City, four small makeshift bombs exploded at a youth centre run by the city's oldest Christian church, breaking doors and shattering glass but causing no casualties. The Greek Orthodox church itself was undamaged.
Coptic pope's criticism
In the first reaction from a top Christian leader, Coptic Pope Shenouda III, the head of Egypt's Coptic Orthodox Church, said in remarks published on Saturday that "any remarks which offend Islam and Muslims are against the teachings of Christ".
"Christianity and Christ's teachings instruct us not to hurt others, either in their convictions or their ideas, or any of their symbols - religious symbols," Shenouda was quoted as saying by Al-Ahram newspaper.
Also in Egypt, about 100 worshippers demonstrated after Friday prayers at the country's prominent al-Azhar mosque in Cairo, chanting: "Oh Crusaders, oh cowards! Down with the pope!"
"Personally, I have no love of the Catholic faith... However, having read the speech, I don't understand what the problem is, he spoke against violence for all religions and called for greater dialogue"
Tim Stokes, UK
One worshipper said: "These Christians are all infidels. Benedict himself is an infidel and a blind man. Doesn't he see that the wars in Iraq and Afghanistan and other places were waged by Christians?"
Hundreds of Egyptian riot police surrounded the mosque, preventing protesters from spilling over into the streets.
In Pakistan, groups held rallies and chanted anti-pope slogans in the capital, Islamabad, and other major cities including Karachi, Quetta, Peshawar and Multan.
Pakistan's foreign ministry summoned the Vatican's ambassador to express regret over the remarks and parliament passed a resolution condemning the comments.
In the US, the Council on American-Islamic Relations, which calls itself the largest Islamic civil liberties group in America, said: "The proper response to the pope's inaccurate and divisive remarks is for Muslims and Catholics worldwide to increase dialogue and outreach efforts aimed at building better relations between Christianity and Islam."
During a speech on Tuesday at a German university, the pope 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'."
Benedict did not explicitly agree with the words nor repudiate them, but went on to say that "violence is incompatible with the nature of God and the nature of the soul".
"These Christians are all infidels. Benedict himself is an infidel and a blind man. Doesn't he see that the wars in Iraq and Afghanistan and other places were waged by Christians?"
Worshipper at al-Azhar mosque in Cairo, Egypt
The Vatican said the pope did not intend the remarks to be offensive, but sought to draw attention to the incompatibility of faith and violence.
But Lebanon's most senior Shia Muslim cleric, Grand Ayatollah Muhammad Hussein Fadlallah, told worshippers in his Friday prayers sermon: "We do not accept the apology through Vatican channels ... and ask him [the pope] to offer a personal apology - not through his officials - to Muslims for this false reading."
Abdullah Ahmad Badawi, the Malaysian prime minister and chairman of the 56-nation Organisation of the Islamic Conference, said: "The pope must not take lightly the spread of outrage that has been created. The Vatican must now take full responsibility over the matter and carry out the necessary steps to rectify the mistake."
But some analysts, such as the Reverend Robert Taft, a specialist in Islamic affairs at Rome's Pontifical Oriental Institute, said it was unlikely that the pope miscalculated how some Muslims would receive his speech.
Analysts said the Catholic leader's speech was a sign that he intends to carry on with his strong defence of the values of the Christian West rather than compromise for the sake of building bonds with Islam.
The Vatican says Pope Benedict
XVI did not mean to offend Muslims
John Voll, director of the Centre for Muslim-Christian Understanding at Georgetown University in Washington, said the speech suggested deep dismay over the conditions of Christians in the Muslim world.
"This reflects the intention of Pope Benedict to distinguish himself from his predecessor on his approach to interfaith dialogue ... it means more reciprocity," said Voll.
As the chief watchdog on Roman Catholic doctrine for his predecessor, Pope John Paul II, Benedict - the former Cardinal Joseph Ratzinger - had little role in shaping the Vatican's contact with Islam and other faiths.
Some say his deep theological scholarship leaves him ill-equipped to deal with Islam at a time when suspicions and tensions dominate relations between the West and Muslim world.
The Reverend Khalil Samir, a Vatican envoy for interfaith links in Lebanon, said: "They went to the speech expecting to meet Pope Benedict, but instead they met Professor Ratzinger."
The full prepared text of the speech can be seen here