The Islamic Cultural Centre said it was protesting against the newspaper's decision to publish a drawing by artist Lars Vilks, whose series of pictures depicting the head of Muslim prophet Muhammad on a dog's body was rejected by galleries in western Sweden.
But not everybody in the Swedish Muslim community has applauded Friday's demonstration - the second in the space of a week.
"I think the demonstration is counterproductive and will only serve to reinforce any prejudices people have about Muslims," Mohamed Omar, editor of Minaret magazine, told The Local.
"Nerikes Allehanda published the picture to illustrate a story. It's irrational to regard their decision to publish as being offensive to Muslims."
Contrary to initial reports, Mohamed Omar says that Minaret never intended to exhibit the pictures, which he regarded as questionable from an ethical standpoint.
"Exhibiting them would have just contributed to anti-Muslim sentiment. Although Nerikes Allehanda had a legal right to publish, I am critical of their decision for the same reason that I didn't want any part in exhibiting the pictures."
The controversy has gained momentum in recent days following official protests from the Pakistani foreign ministry and Iranian president Mahmoud Ahmadinejad.
"Iran and Pakistan are just playing to the Muslim gallery. Ordinary Muslims in Sweden are the ones who have to suffer the consequences."
The Islamic Cultural Centre was not the only group protesting outside Nerikes Allehanda's offices. An hour earlier, representatives from the Liberal Party's youth wing showed for a demonstration in support of freedom of expression.
"We are doing this to protect freedom of expression and freedom of the press. It has come to our attention that there are people don't think people should be able to say what they want and that makes us angry. Freedom of expression is absolutely central," spokeswoman Hannah Ström told TT.