At the same time, hundreds of angry Iraqis have demonstrated in the southern port city of Basra against the Pope, burning an effigy of the pontiff and calling for an apology.
The protestors, followers of Ayatollah Mahmud al-Hassani, a mystic Shiite cleric who says he's in direct contact with Shiite religious figures, also burned German and American flags.
Earlier, the Pope sought to mollify Muslim anger, saying he was "deeply sorry" for the outrage sparked by his recent remarks on Islam, stressing they did not reflect his personal opinion.
The Pope's expression of regret was welcomed by several prominent Muslim groups, which said they hoped his words would calm tensions that have flared throughout the Muslim world.
But other Muslim organisations seemed to reject the Pope's statement as falling short of the full, personal apology they had demanded, with some Islamist groups issuing fresh threats of attacks against Christians.
Pope Benedict had come under mounting pressure from Muslim leaders worldwide to retract his remarks made in Germany last Tuesday in which he quoted a mediaeval text that criticised some teachings of the Prophet Mohammed as "evil and inhuman".
"I am deeply sorry for the reactions in some countries to a few passages of my address ... which were considered offensive to the sensibility of Muslims," the Pope said during the traditional Angelus blessing from the balcony of his summer residence at Castel Gandolfo outside Rome.
He stressed that the passages he quoted during a speech at Regensburg University "do not in any way express my personal thought".
"I hope that this serves to appease hearts and to clarify the true meaning of my address, which in its totality was and is an invitation to frank and sincere dialogue, with great mutual respect," he added.
The Angelus blessing marked the Pope's first public appearance since the furore broke over his university lecture, in which he also implicitly linked Islam with violence.
He said the "true meaning" of what he said in Germany had been earlier clarified by the Vatican's Secretary of State Cardinal Tarcisio Bertone, who had said the Pope's words had been misinterpreted and were meant as a rejection of the religious motivation for violence, "from whatever side it may come".
That explanation had been angrily dismissed by many Muslim groups who insisted on a "clear" papal apology.
Apology welcomed
One of the most vocal critics, Egypt's opposition Muslim Brotherhood, said the pope's expression of sorrow represented "a good step" towards an apology.
"We consider today's statement by the Pope a retraction of what he said last week," Mohammed Habib, a senior member of the group, told news agency AFP.
The Central Council of Muslims in Germany welcomed what it described as "an important step towards calming the unrest of the past days in many parts of the world".
Indian Muslims also welcomed what Maulana Khalid Rashid, a member of the powerful All India Muslim Personal Law Board in Lucknow, called "the apology tendered by the Pope Benedict".
A leading British Muslim group also said it was now satisfied that Pope Benedict XVI had not intended to offend Muslims.
"All the while we've been asking the pope to make it clear he did not share the views of the Christian emperor, which he had in his address at Regensburg University," Muslim Council of Britain spokesman Inayat Bunglawala said.
"Now the Pope has made that clear, we hope things will calm down. It is exactly what we wanted to hear," he said.
However Malaysian Foreign Minister Syed Hamid Albar said Malaysia was not satisfied with the apology and would continue to insist on a full apology.
"Muslims have all this while felt oppressed and the statement by the pope saying he is sorry about the angry reaction is inadequate to calm the anger, more so because he is the highest leader of the Vatican," Mr Syed Hamid was quoted as saying by state news agency Bernama.
He said the pope must retract his statement as he only stated he was "deeply sorry" about the negative reaction.
Iran later said an expression of deep regret did not go far enough and called on the pontiff to admit he had made a mistake.
"The pope was right to give these explanations and he said that his comments were badly reported," government spokesman Gholam Hossein Elham said.
"These explanations were necessary but not sufficient. He needs to say more clearly that what he said was an error and correct it," he added.
China's state media quoted Chen Guangyuan, president of the Islamic Association of China, as voicing "anger and condemnation" over the remarks which he said had "gravely hurt" the feelings of Chinese Muslims.
Meanwhile the Italian interior ministry told police chiefs to raise the level of national security amid violent threats by Islamist groups overseas.
Italian nun shot
As anger ran high in the Muslim world, an elderly Italian nun was shot dead in the Islamist-held capital of Somalia on Sunday, in what Vatican spokesman Federico Lombardi denounced as a "horrible act".
Two gunmen shot and killed the Catholic nun and her bodyguard in an ambush at a children's charity hospital in the city's Huriwa District after a prominent Somali cleric apparently said Muslims should avenge the pontiff's remarks.
The Supreme Islamic Council of Somalia (SICS) quickly condemned the killing as "barbaric and contrary to the teachings of Islam" and said it had detained one of the attackers, who was cooperating in their investigation.
"We are hopeful we will capture the second killer, he has nowhere to hide," SICS deputy security chief Sheikh Muktar Robow told AFP.
He said no motive had been ruled out for the attack, which came less than two days after a hardline Mogadishu imam told Muslim faithful at a mosque in southern Mogadishu to "hunt down" and kill those who insult Islam.
The head of the Vatican press office, Federico Lombardi, said the nun's slaying in Mogadishu was "horrible" and hoped it would remain an "isolated act," Italy's ANSA news agency reported.
Simmering anger
A one-day strike in Indian Kashmir called by hardline Muslim separatists to protest the Pope's recent remarks on Islam saw shops, businesses and government offices closed today.
In the summer capital Srinagar, the urban hub of the anti-India insurgency, traffic was light with most government offices closed in the Muslim-majority state, witnesses said.
Earlier, religious seminaries across Iran shut on Sunday to stage protests over the Pope's "outrageous" remarks, while Morocco said it was recalling its ambassador to the Holy See.
Two armed Iraqi groups posted statements on the Internet urging Muslims toward reprisal, though it was not clear if the threats took the Pope's most recent public expression of regret into account.
And a third day of attacks on Christian places of worship in the
Palestinain territories saw unknown assailants throw Molotov cocktails and a burning tire at two Catholic churches in the northern West Bank.
The head of the Hamas-led government, Ismail Haniya, denounced the attacks and called on Palestinians to exercise restraint.
The scale and intensity of the Muslim reaction had cast doubts on the Pope's next scheduled foreign trip in November to Turkey.
However, Turkish Foreign Minister Abdullah Gul said the visit would go ahead as planned.