The girl was grazed on the back of her head when police fired shots during the protest on Tuesday, said Brigadier Hangwani Mulaudzi.
“Her mother claims that the child was shot by the police during the protest,” Mulaudzi said.
The Independent Police Investigative Directorate (Ipid) would determine who was responsible for the girl’s injury.
The six-year-old was admitted to the Sekororo hospital for observation, said Limpopo health department spokeswoman Adele van der Linde.
Van der Linde said she was not severely wounded but medical observation was necessary due to her age and because it was a head injury.
Service delivery in the area had been compromised due to the protest in the area.
“It is a tense situation as the protesters are blocking many of the roads,” said Mulaudzi.
“Police are doing everything in their means to control the situation,” he said.
Meanwhile, the Sekororo hospital and the Lorraine clinic were also disrupted due to the protest, said Van der Linde.
“Some of the staff were prohibited from entering the clinic, but the clinics are still open,” she said.
Mulaudzi said police were on the scene.