One woman was killed in the battle for Kodori Gorge, but rebel local strongman Emzar Kvitsiani escaped, said presidential chief of staff Georgy Arveladze.
Tbilisi sent troops to the gorge after ex-governor Kvitsiani declared autonomy from the capital.
Kvitsiani's militia had controlled one stretch of the gorge, which is a gateway to the breakaway Black Sea region of Abkhazia. Abkhaz separatists control the southern half of Kodori Gorge under a 1994 deal which ended a civil war.
"Law and order is restored in the gorge," Arveladze said. "The anti-criminal police operation is successfully finished. Right now, the search operation is going on for a few criminals who are hiding in the woods. We will get them, it's just a matter of time."
Arveladze said soldiers killed one woman in a skirmish with rebels, but blamed her death on Kvitsiani supporters.
"That happened because Kvitsiani and his people were hiding behind civilians' backs," he told a news conference.
Arveladze said only two servicemen were lightly wounded in the operation.
The clashes in the gorge -- one of the routes Georgian troops took in a failed attempt to re-establish control over Abkhazia in 1992-93 -- have alarmed Abkhaz separatists, suspicious of any military buildup by Tbilisi in the area.
Separatist leaders in Abkhazia, echoed by their Russian allies, say Tbilisi could use the operation to concentrate forces in the gorge and then use it as a springboard for a strike to regain control of the province.
"They are creating a bridgehead to move toward Sukhumi along the shortest track," Interfax quoted Lieutenant General Valery Yevnevich, head of Russia's peacekeepers in the region, as saying.
Georgia has promised its operation against Kvitsiani will not spill over into Abkhazia.
Abkhaz leader Sergei Bagapsh has said his forces, concentrated in the separatist-controlled part of the gorge, were under orders to open fire if Georgian troops "cross the border even by one meter."
Russia, who's peacekeepers in the area are on high alert, has warned Georgia against violating the 1994 cease-fire deal. Georgia has responded by accusing Russia of trying to annex its territory and demanding Moscow's peacekeepers leave. Georgian officials have announced a 100,000 Georgian lari ($58,000) reward for information leading to Kvitsiani's capture.
Georgia's relations with Russia have grown worse under pro-Western President Mikheil Saakashvili, who wants to end Georgia's dependence on Moscow and join NATO.
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