In the Gaza Strip, Hamas joined in the condemnation, saying the cartoon was an "offence to the feelings of tens of millions of Muslims".
The Palestinian organisation called for those responsible to be put on trial.
It also called on Arab and Muslim governments to "use those means of pressure available to them to put an end to the organised campaigns aimed at spreading hatred against Islam in the name of free expression".
In Karachi, Pakistan,students chanted slogans and burned a Danish flag.
Newspapers reprinted the provocative drawing on Wednesday in protest at an alleged plot to murder one of the cartoonists.
The publications defended their decision saying they were upholding freedom of expression.
A Danish citizen of Moroccan descent and two Tunisians were arrested on Tuesday as suspects in a plan to kill Kurt Westergaard, a cartoonist at Jyllands-Posten, the Danish newspaper that originally published the drawings in September 2005.
Danish media said the man of Moroccan descent had been released but faced preliminary charges.
The Tunisian men, who have been legal residents in Denmark for more than seven years, were ordered to be expelled without trial by the Danish justice ministry on grounds of national security.
The two on Thursday said they would appeal against the expulsion order.
In Copenhagen, 17 youths were arrested after a fourth night of riots in a predominantly immigrant area of the Danish capital, police said.
A spokesman said the riots could be linked to the cartoon or to the planned expulsion of the two Tunisians.
Iran summoned Denmark's ambassador on Wednesday to protest against the reprinting of the cartoon.
Iran's state news agency IRNA said: "The foreign ministry summoned the Danish ambassador following the repetition of the insults to the Prophet and in order to voice an official protest.
"The foreign ministry... strongly condemned this and urged a serious confrontation against such insults and a prevention of any repetition."
Hundreds of Iranian demonstrators briefly stormed the Danish embassy twice in February 2006 and threw Molotov cocktails.
In October 2006, demonstrators upset by a satirical video of the Prophet Muhammad aired on Danish television also threw firebombs and rocks at Denmark's embassy in Tehran.