The boys belonged to the church’s pastor, who said that the incident occurred after his older son got hold of a gun in the back of a parked car.
Officers from the Burke County Sheriff’s office received reports of a shooting at the River Valley Baptist Church just before 8.30am on Sunday.
After being assessed by Emergency Medical Personnel (EMP), the toddler was flown by helicopter to a hospital in Charlotte.
On Monday police said the boy was undergoing surgery and remained in critical condition. The force added that the investigation was ongoing, and that further information would be released in due course.
Footage from the scene showed a shower of broken glass in the car park. Local outlet WYFF reported that the pastor had confirmed it was his son who had shot the two-year-old by accident.
The pastor said the bullet did not hit the toddler’s brain, and he is still able to talk and move, according to WYFF.
Neighbours told the outlet they had heard the gunshots and screaming in the immediate aftermath.
Congregation member Kevin Barlow said: “Our hearts go out to them – we’ll help in any way we can. But God is the help that you need.”