The president stated on Monday that the "current crisis in South Ossetia is not a problem between Georgians and Ossetians. This is a problem between Georgia and Russia."
Saakashvili went on to charge that "certain forces in Russia" are preparing for "aggression against Georgia," the website Civil Georgia reported.
Calling on Putin to "restrain these forces", Saakashvili warned that any armed conflict in South Ossetia would not be a fight between Georgians and Ossetians, but would become "a serious problem between the two countries, Georgia and Russia."
His statements mark a sharp departure from previous declarations that relations between Russia and Georgia had entered a "new stage" of understanding and cooperation.
As he boarded a flight to London, Saakashvili claimed that South Ossetian leader Eduard Kokoev and his Russian backers are planning to provoke a conflict.
He referred to a recent air space violation on Saturday, when a Russian ME8 aircraft flew over the Georgian border from Chechnya, an action Saakashvili said he hoped was "an accident".
The Georgian government has also charged that the Roki Tunnel, a roadway connecting the Russian autonomous republic of North Ossetia with South Ossetia, has been used to move military equipment into the disputed territory.
In a 4 July interview with Interfax, Saakashvili declared that Georgia wants to establish a border checkpoint at the tunnel to take control of the travel route.
But Moscow disputes Tbilisi’s claims, and continues to maintain that Georgia alone is responsible for the crisis in South Ossetia.
Speaking to reporters in the Russian capital on 11 July, Foreign Minister Sergei Lavrov charged that Georgia had "illegally brought into the conflict zone hundreds and thousands of armed forces who do not come under the peacekeepers' control," Interfax Russia reported.
The "current crisis
in South Ossetia is
not a problem between Georgians and Ossetians. This is a problem between Georgia
Lavrov put the number of these alleged armed forces at "up to 3000".
On Saturday, a Russian Foreign Ministry statement claimed that the Joint Control Commission - the quadripartite body charged with preserving peace and security in South Ossetia - was also addressing the issue of "illegally deployed Georgian military units".
It called on all parties to refrain from "setting up any posts in the conflict zone without the commission's agreement."
Russia, Georgia, South Ossetia and North Ossetia all retain representatives on the commission.
Lazrov went on to tell reporters that Russia would be justified in breaking up "illegal formations" in South Ossetia, an action that would no doubt be seen as a provocation by Tbilisi, which views South Ossetia as part of Georgian territory.
However, at the conclusion of his 2-4 July summit with Vladimir Putin, Saakashvili told Interfax that the Kremlin had pledged not to interfere in the country’s "internal affairs".