The boy's bag was searched, but no weapon was found, Richneck Elementary school superintendent George Parker told parents.
First-grade teacher Abigail Zwerner was left with serious injuries after police say the boy shot her "intentionally".
Police said he used his mother's gun.
The shooting has rocked the town of Newport News and raised questions about what legal ramifications the young boy could face for carrying out the shooting."At least one administrator was notified of a possible weapon," Mr Parker said during an online meeting with parents on Thursday, according to a clip shared by local news outlet WAVY-TV. "(The staff member) was aware that that student had, there was a potential that there was a weapon on campus."
The school superintendent did not clarify whether the boy hid the weapon or why authorities did not find it in his backpack.
The BBC has contacted the school superintendent for comments.
After the shooting, police said they found a 9mm Taurus pistol in the class near the student's desk, along with his backpack, a mobile phone and one spent shell casing.
Police determined through an interview with the child's mother that the gun was bought legally and stored in their home.
The shooting happened without warning, and with no fight or physical struggle, police said.
Newport News police chief Steve Drew said the child fired one round at his teacher. He added that the "shooting was not accidental, it was intentional", and that it took place while Ms Zwerner was giving a lesson.
The school remains closed after the incident.
Ms Zwerner was in serious but stable condition earlier this week, authorities said.
The school is making administrative changes in the wake of the incident and has consulted with Robb Elementary School in Uvalde, Texas, where a shooter killed 19 children and two adults last year.
The school district is installing metal detectors at every campus and will hold a safety training day where staff can discuss additional security measures, school board Chair Lisa Surles-Law said at a news conference Thursday.
Daily metal detector for checks for students remain rare, taking place at fewer than 2% of public elementary schools in 2020, according to National Center for Education data.
The district has not yet said when Richneck will reopen. The six-year-old boy is being held at a medical facility.
Police have lauded Ms Zwerner for her determination to escort all of her students out of the classroom after she was shot.