The deputy, Joe Martin, had gone to Augusta Estates mobile home park on Milledgeville Road to investigate a burglary.
While taking a statement, he noticed another man whom he recognized as Diriuss Antonio Redd, who had five warrants out for his arrest, three of which Martin had issued, investigators say.
Martin immediately got into his cruiser and pursued Redd.
Sheriff's Maj. Ken Autry said a "struggle" ensued that ended with Redd shot in the "midsection." Autry did not know whether the deputy intentionally fired his weapon or whether it went off accidentally during the struggle.
"It looks like he was justified either way because the guy was trying to get his weapon," Autry said.
He said Redd's injury "didn't appear life-threatening."
Several people in the neighborhood who heard the commotion said Martin yelled "get down," and one shot was fired.
Resident Stephanie Kelly said Redd was struck in the buttocks.
Redd was wanted on four misdemeanor warrants and one felony, which Autry said was stalking-related.
Martin, 47, was a Richmond County sheriff's deputy in the 1990s and returned in October. Autry said he didn't know what Martin did in the interim but said, "He's not a rookie."
Martin will remain on administrative leave while the Georgia Bureau of Investigation investigates.