The Vesti TV channel reported earlier that two people had been killed in the incident in Tskhinvali, where over 15 mortars were fired at the capital.
"According to preliminary reports, three people were killed and around 11 people injured in an escalation [of the situation] and a special Georgian military operation," the state website said.
Georgia fired in three directions "using mortar, grenade launchers and fire arms." The villages of Ubiat and Dmenis were also attacked, alongside Tskhinvali, South Ossetia said.
The joint peacekeeping forces deployed in the Georgian-South Ossetian conflict zone have been put on high alert, the Vesti channel said.
Tbilisi and Russian-led peacekeepers are currently deployed in the region.
South Ossetian President Eduard Kokoity has warned that military hardware will be moved into the conflict zone if the incident is repeated.
South Ossetian units "will open fire only as a last resort and on my personal instruction. All of the enemy's firing positions have been located and will be eliminated at any moment," Kokoity said.
Although the Georgian Interior Ministry has so far failed to comment on the incident, military observers from the Joint Peacekeeping Forces and officers from the OSCE mission have already confirmed reports of the attack.
However, according to unofficial police sources in Georgia's Shida Kartli region, bordering on the conflict zone, Georgian police outposts came under fire from South Ossetian villages in the conflict zone. Georgia returned fire, after which shelling continued for several minutes.
South Ossetia said Thursday a checkpoint on its de-facto border came under fire from the Georgian side, and one police officer was wounded. The incident followed three sets of explosions that injured six people earlier this week in Georgia's other separatist province, Abkhazia.
South Ossetia declared its independence from Georgia following the collapse of the Soviet Union in 1991. A bloody conflict that followed killed hundreds of people. The pro-Western Georgian leadership has said it is determined to bring the breakaway region, along with the rebel region of Abkhazia, back under central control.
