Jamesburg school superintendent Gail Verona told The Home News Tribune of East Brunswick the lighter had the potential to compromise student safety.
But the 11-year-old boy's father questioned why school officials consider the lighter a weapon.
Patrick Halpin called police Wednesday to say there were weapons on school property because teachers at the Grace Breckwedel Middle School had lighters in the building.
Halpin says he was a "little irate" because his son, who is a Boy Scout, never flicked the lighter.
The superintendent says a weapon is anything that "has the potential to cause harm."
Jamesburg Police Chief Martin Horvath says he believes the school took appropriate action.