Irakly Okruashvili told Georgia's Rustavi-2 television over the phone from the Kodori Gorge that troops had to complete the "mopping-up of criminals from the area."
Georgian authorities earlier declined to confirm that Okruashvili was in the gorge, leading the special operation together with Interior Minister Vano Merabishvili.
Okruashvili said Tbilisi had re-asserted its authority in the area and added that Georgian security forces had taken control over all the towns and villages in the gorge, where tons of weapons and ammunition had been seized.
Police forces will control and patrol the Kodori Gorge from now on, he said.
Before the conflict, a Hunter battalion of the Defense Ministry, led by Emzar Kvitsiani, had been maintaining order in the district but it was formally disbanded in 2005 after President Mikheil Saakashvili came to power, though most members had refused to lay down arms.
The Kodori Gorge is in northern Georgia and is the de facto border between the self-proclaimed republic of Abkhazia and the Georgian-controlled territory. The gorge is cut off from the rest of Georgia due to lack of infrastructure and transportation, as well as its mountains and forests.
Okruashvili also said Kvitsiani had led the rebellion of a local militia group "following orders of some outside force."
On Sunday, former presidential envoy Kvitsiani said he refused to recognize Tbilisi's rule in the area and to disarm his Hunter battalion. Tbilisi responded with a military operation Tuesday to re-establish control over the area. A reward of $55,000 has been offered for information leading to Kvitsiani's capture.
