The fire was started at a bus shelter on the Vivalla estate shortly before 3am, the newspaper reports.
"The fire was intentional. Newspapers don't just burn by themselves," police spokesman Thomas Ginghagen told Nerikes Allehanda.
Some 200 to 300 newspapers are reported to have gone up in flames. Police have not made any arrests in connection with the incident.
It is the second time in a few days that copies of the newspaper at the centre of the Muhammad caricature row have been destroyed. At the weekend a number of newspapers were thrown into a fountain in protest.