Police fired teargas and rubber bullets to disperse hundreds of demonstrators in Pakistan's capital on Sunday, despite sealing the city to stop protests against the cartoons.
Almost five months after publishing 12 cartoons of the prophet to highlight what it described as self-censorship, the Jyllands-Posten newspaper printed a full-page statement in a pan-Arab newspaper.
It was the strongest expression of regret from the newspaper, but stopped short of saying sorry for printing the cartoons, instead, apologising for the turmoil they caused.
"These drawings apparently hurt millions of Muslims around the world, so we now offer our apology and deep regret for what happened because it is far from the paper's intention," said the statement in the Saudi-owned Asharq al-Awasat titled "Apology" in big bold letters.
"We did not set out to offend or insult any religion. We apologise for being misunderstood and reiterate that we did not intend to target anyone ... I hope this clears the misunderstanding and God bless," the statement said.
At least 32 people have been killed and dozens wounded since Tuesday in riots over the cartoons that swept through Libya, Nigeria and Pakistan.
Muslim religious and civic leaders across the world have insisted anger will be quelled only with a clear and unequivocal apology from the newspaper and the Danish government for the cartoons, considered blasphemous by most of the world's estimated 1.3 billion Muslims.
Protests have turned violent
Others have said it is too late for an apology, calling for legislation in Europe that would outlaw caricaturing or insulting religious symbols.
After the deaths of five Pakistanis in riots last week, an alliance of six Islamic parties known as Muttahida Majlis-i-Amal (MMA) said they would defy the ban despite the lockdown in Islamabad.
Despite police cordons, teargas and warning shots, about 1000 protesters managed to congregate near a central bazaar where they chanted religious and anti-government slogans.
Aside from the usual chant of Allahu akbar, or God is greatest, demonstrators lampooned the Pakistani president, Pervez Musharraf as a lackey of George Bush, the US president.
"Bush has reared a dog wearing a uniform," they chanted, referring to Musharraf's broken promise to the MMA that he would give up his dual role as president and chief of the armed forces, and to his alliance with Washington in a war on terrorism.
Police and paramilitary troops patrolled streets in Islamabad, while barbed wire was placed across main routes leading to parliament and elsewhere.
But nearly 100 protesters broke through the cordons and were joined by hundreds of others from side streets.
Police fired teargas, and when the protesters retaliated by throwing stones, police responded by firing warning shots into the air and what a local official said were rubber bullets into the crowd.
Qazi Hussain Ahmad (C) was
arrested ahead of the protest
Earlier, on Sunday morning police put MMA president Qazi Hussain Ahmad under house arrest in Lahore before he could
travel to Islamabad to lead the march.
MMA supporters burned tyres on roads in the nearby city of Rawalpindi, where police had earlier detained more than 100
The Danish Foreign Ministry said on Sunday its ambassador had come home temporarily, having shut the embassy in Islamabad two days earlier because of the security risk.
Fearing further sectarian violence after the deadly riots a day earlier, Nigeria drafted in police and troop reinforcements to enforce a curfew in two cities in the north, which is mostly Muslim.
Fifteen people were killed on Saturday when Muslims protesting against the caricatures in the Borno state capital, Maiduguri, turned on the Christian minority, burning shops and churches, police spokesman Haz Iwendi said.
"These drawings apparently hurt millions of Muslims around the world, so we now offer our apology and deep regret for what happened because it is far from the paper's intention"
Statement by Jyllands-Posten
A protester was killed and several injured when police in the city of Katsina opened fire on a crowd of stone throwers, he said.
"Police and military personnel are on the streets in joint patrols to ensure that there's no repeat of the unrest," local reporter Abdullahi Bego told AFP by telephone from Maiduguri.
"It's Sunday, and Christians are going to church, and so there is fear that someone might try to foment trouble," he added.
Eleven Libyan protesters were killed on Saturday and 35 others injured in violent demonstrations that led to the torching of the Italian consulate in Benghazi.
The demonstration was in response to Italian Reform Minister Roberto Calderoli donning a T-shirt that reprinted the prophet caricatures.
Calderoli was pressured into resigning by Italian Prime Minister Silvio Berlusconi over the affair, while the Libyan security minister and other officials were sacked for excessive use of force in Benghazi.