CNN is reporting:
An "electronic threat" received early Tuesday prompted the decision, school district police Chief Steve Zipperman said, adding that the threat "is still being analyzed."
District superintendent Ramon Cortines explained the "message" referred to backpacks and "other packages." He said many schools were threatened, though none by name. The threat was toward students in schools (as opposed to on buses).
So probably an email or emails sent, not just one call or calls made by a student/s.
Every School in the district is being searched. 640 thousand students affected.