By Lada Yevgrashina

BAKU, June 19 (Reuters) - Georgian President Mikhail Saakashvili vowed on Tuesday to resolve a conflict in the breakaway region of South Ossetia and warned the region's separatist leader that his days in power were numbered.

South Ossetia, a sliver of land in the Caucasus mountains, broke away from Georgia in the 1990s and is propped up by Russia after a conflict that prompted thousands of Georgians to flee.

"Resolution of the conflict in South Ossetia is a matter of a short period of time ... a matter of several months," Saakashvili told a news conference in the Azeri capital Baku.

"I'd like to warn comrade Kokoev that his time is nearing an end," Saakashvili said, referring to the region's pro-Russian separatist leader Eduard Kokoity. "The stop-watch has been switched on."

Saakashvili has vowed to restore control over both South Ossetia and Abkhazia, another breakaway region.

Moscow and Tbilisi have traded barbs over the regions since the 1991 fall of the Soviet Union.

Georgia's ties with its giant neighbour dived to the lowest level for a decade last year after a spying row, trade disputes and harsh rhetoric on both sides.

Clashes between pro-Russian and Georgian forces are frequent and some analysts suggest tensions in South Ossetia could rise ahead of Russian elections later this year.

"We count on the constructive role of Russia in this process," Saakashvili said, speaking after meeting leaders of the GUAM organisation, which also includes Georgia, Ukraine, Azerbaijan and Moldova.

Russia says its peacekeepers prevent an ethnic bloodbath in the regions and 99 percent of roughly 50,000 voters last year said "Yes" in a referendum on separation from Tbilisi.

Georgia says the regions are part of its territory and that criminal gangs exploit the areas for smuggling.

Georgia's parliament in April supported a proposal from Saakashvili to create a temporary administration in South Ossetia to give a boost to pro-Tbilisi politicians, who are led by Dmitry Sanakoev.

Moscow has criticised the move, saying it would raise tensions in the region.

"We'll start negotiations with Sanakoev's government in the nearest future," Saakashvili said. "We'll give Ossetians all they want within the Georgian state."

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