The school's principal has apologized for the incident, according to a spokeswoman.
Abdirizak Aden said the teacher at Shiloh Middle School in Georgia, stopped his 13-year-old daughter, who wears a hijab, and asked if she had a bomb.
Aden told The Atlanta Journal-Constitution that his daughter was extremely upset by the comment and he went to the school to see what had happened.
"I was upset," said Aden, who works as a truck driver and grocery store owner. "I was going to take my daughter out (of that school)."
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Sloan Roach, a Gwinnett County Public Schools spokeswoman, told the newspaper that the school's principal has apologized to the family.
"The remark was not appropriate, but based on their conversation and investigation," school officials don't believe it was made with "ill intent," Roach said.
She said the comment came as the teacher was urging students to put away their backpacks.
The incident "shows the level of Islamophobia impacting people's relationships with one another," Yusof Burke, board president of the Georgia Chapter of the Council on American-Islamic Relations, told the newspaper.