Some 120 pupils around the age of 15 and their teachers at the Korsavad school in Simrishamn had posed for a picture together for their yearbook last autumn, reported regional newspaper Ystads Allehanda on Thursday.
But when the photographer later processed the pictures he discovered that a number of pupils appeared to be doing Nazi salutes in at least one of the photographs.
He contacted principal Pia Svensson who pulled the picture from the yearbook and contacted the boys' parents.
After speaking to the pupils the school decided to report the incident to the police.
The boys have denied any criminal offence, however the prosecutor argues that they had been “in mutual agreement to express contempt for a group of people” by making the gesture, according to broadcaster SVT.
Earlier this week the Swedish town of Vetlanda hit out after a Nazi swastika flag was hoisted from one of the official flag poles at the town hall to coincide with Adolf Hitler's birthday.
The council told The Local that the offensive banner had been removed as soon as it was discovered.
“We take this very seriously. Vetlanda should be an open and welcoming council and these types of symbols are completely unacceptable to us. We're reporting it to the police,” it said in a statement.
Last month a man who made Hitler salutes in Umeå was fined for inciting racial hatred.