The auditorium was closed immediately following the discovery of the second swastika Thursday for removal, Superintendent Nick Norcia said in an email to parents.
Last week, a swastika was found carved into a bathroom stall in the boy's locker room, Norcia said.
"As I stated last week, hate-based behavior is intolerable and has no place in society and in our schools," the email said, noting Fair Lawn police are investigating.
Norcia called the initial incident "shocking and disturbing," noting it was an unfair representation of the Fair Lawn community.
Glen Rock police were investigating a similar incident this week as well.
A presentation addressing bias, prejudice and stereotypes was in the works, he said.
"In response to these recent instances at MMS, you can be assured that we are making this a top priority and as soon as we have an educational agenda, we will communicate it to you," Norcia said.
"Safety, security and respect for all are our top priorities for the district community."
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