Protesters, some chanting slogans and carrying banners, marched several blocks under rainy skies to the newspaper's office.
Jamal Lamhamdi, the leader of the Islamic cultural centre in Oerebro, held a 15-minute meeting with the Ulf Johansson, the editor-in-chief of Nerikes Allehanda, Carlson said.
Meanwhile, a small group of demonstrators staged a counter-protest, their mouths symbolically gagged.
The publication of the cartoon prompted angry reactions from Iran and Pakistan, which have both summoned Swedish diplomats to receive protests.
The 57-nation Organisation of the Islamic Conference has also condemned the publication and urged the Swedish government to punish the artist and the publisher as well as demand an apology.
Fredrik Reinfeldt, the Swedish prime minister, told the TT news agency on Friday that he would defend Sweden's "freedom of expression, which is written into our constitution and ... which means that we don't make political decisions about what is published in newspapers."
The cartoon was drawn as part of a series by Lars Vilks, a provocative Swedish artist.
Several art galleries have refused to display the sketches because of fears of angry reactions from Muslims.
Vilks said he had received "several death threats by telephone, email, and comments to my blog" and that he planned to file a police complaint and seek protection.
The cartoon's publication comes a year after deadly riots in several countries against 12 cartoons of the Prophet Mohammed published in Denmark's biggest daily newspaper.