The protest concerned a cartoon by artist Lars Vilks, which showed the head of Muhammad on the body of a dog. In a statement, the Ministry of Foreign Affairs in Islamabad said Pakistan condemned the publication "in the strongest terms."
"Regrettably, the tendency among some Europeans to mix the freedom of expression with an outright and deliberate insult to 1.3 billion Muslims in the world is on the rise," the statement said.
The Swedish Chargé d'Affaires in Islamabad, Lennart Holst, was given a dressing down on Thursday by Miangul Akbar Zed, a middle-ranking official at the Pakistani Foreign Office. The official protest was relayed during the course of a planned meeting.
According to the Pakistani statement, Holst said the Swedish government "fully shared the views of the Muslim community" and called the publication on August 18th "unfortunate."
Swedish Foreign Ministry spokeswoman Anna Björkander told The Local it had been a "misunderstanding" on the part of the Pakistanis to conclude that the government fully shared the views of the Muslim community.
Björkander added, however: "The Chargé d'Affaires said he was sorry if the publication had hurt Muslim feelings."
She also said that Holst had told the Pakistani official that freedom of the press is strongly protected in the Swedish constitution.
"Otherwise the Swedish government has no opinion on the matter," she said.
Nerikes Allehanda editor Ulf Johansson told The Local that it would be "strange" if the Swedish Chargé d'Affaires had apologized over the cartoon, and would contradict the Swedish government's previous line of not interfering with press freedom.
"We have noted this and contacted the Swedish Foreign Ministry for an explanation," he said.
Johansson said that he was not particularly concerned by Pakistan's intervention.
"The most important thing for me is our relations with the local community here. I am less interested in what foreign governments have to say."
A demonstration was held outside Nerikes Allehanda's headquarters in Örebro on Friday, and another is planned tomorrow.
Johansson said that Friday's demonstration was peaceful, with demonstrators shouting slogans and brandishing placards.
The complaint from Pakistan comes several days after a Swedish diplomat in Teheran was summoned by the government there to face a similar protest.
Pakistan says it plans to consult with the Organization of Islamic Conferences to determine its future course of action when cartoons of the Prophet Muhammad were published.