Ben Chance, a longtime employee of Don's Guns and Galleries, was reported in critical condition after the shootout Monday, The Indianapolis Star reported.
Don Davis, the store owner, said Chance was expected to survive his injuries.
Police said Brian C. Wayner rented a gun Monday afternoon and used it for target shooting at the store's firing range. When he was done, he allegedly returned to the counter and opened fire on Chance with no warning or explanation.
Davis said customers are only supposed to have loaded guns in the range area. He said any employee would have responded as Chance did.
"If you shoot us, we'll shoot you right back," he said.
Don's Guns has had other brushes with violence, including a customer who used a rented weapon to kill himself at the store.
In 2010, The Washington Post said 1,910 weapons used in crimes were traced back to Don's Guns in four years, the third-highest total in the country. A 2000 report by a gun-control group said Don's Guns ranked second in the previous four years in guns used in crimes.