Deborah Farley, 53, admitted she put the pistol in the backpack along with ammunition and a flare gun, the New York Daily News reported, citing sources.
She said she forgot to remove them before her son left for school.
Farley faces several charges, including criminal possession of a weapon and endangering the welfare of a child.
Farley had gone to Wave Preparatory Elementary School in Far Rockaway Thursday morning, but told school officials only that she had to take the boy out of class for a dentist appointment -- and only acknowledged he had weapons after he told her he had given a gun to another boy, the report said.
Walter Orozo, the boy's father, said the 7-year-old was afraid of bullies at school, the Daily News reported.