Shota Utiashvili, the spokesman for the Georgian interior ministry, confirmed the removal of the checkpoint, where 20 to 30 Russian soldiers had been deployed.
"It looks like the start of the withdrawal.," he said. "Georgian police are moving into the area immediately."
Alexander Lomaia, the Georgian national security council secretary, said Russian troops had also been seen apparently preparing to leave another checkpoint, at Perevi near the border with South Ossetia.
"In Perevi, the Russians are making some preparations, possibly for a withdrawal," he said.
Russian has agreed to withdraw its forces from so-called "security zones" around South Ossetia and Abkhazia, another rebel region, under an EU-brokered peace deal.
The deal followed a five-day war between Russian and Georgia in August.
At least 200 unarmed EU monitors have been in the buffer zones since October 1 to observe the ceasefire and Russian withdrawal.
Russian forces entered into Georgian territory during the conflict, as well as the breakaway pro-Russian regions of Abkhazia and South Ossetia.
The conflict was ignited by months of sporadic fighting between separatists and Georgian soldiers.
The Georgian military attempted to regain control of South Ossetia, at which point Russia sent in its military, pushing Georgian troops back to within their own border.
Moscow said that it was protecting its citizens in the area from Georgian aggression.
However, Tbilisi said that Moscow provoked the conflict and Western powers said that Russia's response was "disproportionate".