The drill, aimed at testing the reactions of faculty and first responders during a simulated attack, included an imaginary scenario that has some Christians up in arms.
During the simulation, two mock gunmen from a fake right-wing fundamentalist group called the "New Crusaders" — a group that does not believe in the separation of church and state — stormed the school. The idea was that they were angry that one of their daughters was expelled for praying before class.
Nobody from the school, including from the superintendent's office or the police department, was willing to talk about the drill on camera, but the township issued a statement saying the chosen scenario was never intended to offend any group and was meant to be generic in nature.
"The term 'Christian' was not included in the scenario. It was believed that all groups pray and prayer in school is a universal issue," reads the statement from the school.
"Similarly it is further believed that all groups experience right-wing fundamentalists in their organizations. The bottom line was the protection of human life should a significant event unfold."
The spokeswoman for the school told FOX News that any "perceived insensitivities" to any religious community are "definitely regrettable."
"It was certainly not the intent to portray any group in a negative manner," said Liz Scott. "The district cherishes and we respect and celebrate the diversity of culture and the faith that exists within our community. Our schools have respected and supported staff members and our students' right to pray."
But critics say even though the word "Christian" wasn't stated explicitly in the scenario, which was created by the Burlington Police and the township public safety director, it is offensive and clearly implied the fake gunmen were Christians.
"Those kinds of buzzwords, 'crusader' — that's Christian only — 'right-wing fundamentalists,' 'separation of church and state,' 'praying' … all those phrases together, buzzwords equal 'Christian,'" said Bob Pawson, the national coordinator of the Scriptures in School Project.
Pawson also said the scenario was not realistic.
"This is an unreal scenario, like I said. No child can be expelled for praying in a school since it's legal; therefore, the parents wouldn't have gotten mad, they wouldn't have used guns. If a school district had expelled a girl for praying in class, the parents would have shown up with attorneys, not with pistols."
The school says critics are blowing things out of proportion and that only about a half-dozen students participated in the drill. But the other side says it's religious ignorance and there's no excuse for it.
FOX News' Lauren Green contributed to this report.