The fire was put out within an hour, but one building was completely destroyed. The shelter was supposed to house about 120 refugees but can now only accommodate 75 people.
"We're lucky no one was injured. It's unbelievably tragic that something like this could happen. We depend on these buildings to be able to give shelter to refugees who come here," Johanna Uhr at the Swedish Migration Board tells Swedish Television News.
Police are still investigating what caused the fire but they believe it was started deliberately.
"We suspect arson," police spokesperson Jenny Widén told Radio Sweden.
Yet another planned refugee shelter was vandalised Saturday, close to Jönköping in central Sweden. Several windows were smashed and stickers with xenophobic messages were put up on the walls of the building.