"Someone threw a firebomb, a Molotov cocktail at the building," Torsten Hemlin a spokesman for Uppsala police told Swedish news agency TT, adding that the bomb did not set the mosque in eastern Sweden alight.
"They also wrote some vulgar racist words," he said, adding that no one was in the building at the time of the attack.
Police in Sweden's fourth largest city Uppsala were alerted by passers-by who reportedly saw a man throw a burning object at the mosque at around 0430 GMT.
Today's attack came just three days after a late night blaze at a mosque in Esloev in southern Sweden which police suspect was also arson.
On Christmas Day five people were injured when a petrol bomb was thrown through the window of a mosque in Eskilstuna, east of the capital Stockholm.
The country's leftist Prime Minister Stefan Loefven called the Christmas attack a spurt of "hateful violence" and said Sweden would "never tolerate this kind of crime".
The attacks come as debate intensifies in the country over immigration and the integration of asylum seekers in the traditionally tolerant Nordic country.
Last month the far right Sweden Democrats -- which doubled its support to 13 per cent in September elections -- came close to bringing down the left-green government over its liberal refugee policies, further boosting its support in opinion polls.
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