Although the mosque has been vandalized before, mosque representative Mahmoud Khalif said the graffiti had not been political previously.
"It is the first time it's been this way, it is usually normal graffiti but this is quite special," Khalif told the Aftonbladet newspaper.
The swastikas were discovered Thursday morning covering the men's entrance to the mosque.
The incident has been reported to police, who are investigating it as a possible hate crime.
"It is a prioritized case when it happens in such a place and with the winds blowing in society at the moment," Stockholm police spokesman Mikael Pettersson added.