Around 200 demonstrators from Muslim groups turned out in Kuala Lumpur to protest the caricatures which depict the prophet as a dog. The demonstrators handed over a letter of protest to Sweden's ambassador in Malaysia, Helena Sångeland.
"They want to protest against the the publication of Lars Vilks' drawings in Swedish newspapers. Their demand is that the Swedish government acts against the Swedish newspapers which published the pictures and also against Lars Vilks," Helena Sångeland told news agency TT.
The demonstration ended with the pulling down of the Swedish embassy's flag, which was then burned.
"It was very surprising and something that we can not tolerate. We have reported the matter to the police," Sångeland said.
According to the ambassador the youth league for the main Islamic party, PAS, and several other Muslim organisation threatened a boycott of Swedish products in demonstrations held a couple of weeks ago.
A smaller demonstration with only a handful of participants was held outside the embassy on Thursday. On that occasion the Malaysian right-wing group Pertubuhan Pribumi Perkasa Malaysia (Perkasa) handed over a protest letter.
Despite angry reactions from many in Malaysia, the ambassador does not consider there to be any risk for Swedish visitors to the country.
"Absolutely not. Nor can I see that our bilateral relations should change because of this," she said.
The controversy started when Swedish regional daily Nerikes Allehanda published Vilks' satirical cartoon in 2007 to illustrate an editorial on the importance of freedom of expression.
The cartoon prompted protests by Muslims in the town of Örebro, west of Stockholm, where the newspaper is based, while Egypt, Iran and Pakistan made
An Al-Qaeda front organisation then offered $100,000 to anyone who murdered Vilks - with an extra $50,000 if his throat was slit - and $50,000 for the death of Nerikes Allehanda editor-in-chief Ulf Johansson.
The protests in Sweden echoed the uproar caused in Denmark by the publication in September 2005 of 12 drawings focused on Islam, including one showing the prophet Muhammad with a turban in the shape of a bomb.