Georgian-Russian relations deteriorated seriously during the September-October 2006 Georgia-Russia spying row when Georgia detained four Russian officers on spying charges. Russia responded by imposing economic sanctions on Georgia and withdrawing its embassy from Tbilisi.
During the spying row, the Russian authorities started to deport Georgian citizens from Russia on charges of visa violations. The government of Georgia as well as the influential human rights organizations such as Freedom House and Human Rights Watch accused the Russian authorities of "tolerating and encouraging the mistreatments of immigrants from Georgia and other Caucasus countries." and of "a deliberate campaign to detain and expel thousands of Georgians living in Russia." On 27 March 2007, Georgia filed an interstate lawsuit with the European Court of Human Rights over the cases of violations of the European Convention for the Protection of Human Rights and Fundamental Freedoms in the course of the deportation of Georgian citizens from Russia in autumn of 2006. Russia described this as a "new unfriendly step taken against Russia".
In March, a village in the Georgian controlled area of Abhkazia was according to Georgia attacked by three Russian helicopters. Russia denied the allegations.
On August 7, 2007, a missile landed in the Georgian-controlled village of Tsitelubani, some 65 km north of Tbilisi. Georgian officials said that two Russian fighter jets violated its airspace and fired a missile, which fell on the edge of a village but did not explode. Georgian President Mikhail Saakashvili said the incident was part of a pattern of Russian aggression against its neighbors and urged European states to condemn Moscow. Georgia claimed to have radar evidence proving that the invading aircraft flew in from Russia and said that the strike had aimed, unsuccessfully, at destroying radar equipment recently installed near the South Ossetian conflict zone.
South Ossetian President Eduard Kokoity described the incident as "a provocation staged by the Georgian side, aimed at discrediting Russia", claiming that another bomb fell in South Ossetia. In his words, "a Georgian military plane crossed into South Ossetia on Monday, performed manoeuvres above Ossetian villages and dropped two bombs."
Russia also denied the Georgian claim. and said that Georgian jets may have fired the missile on their own territory as a way of provoking tensions in the region and derailing a session of the Joint Control Commission on Georgian-South Ossetian Conflict Resolution. Georgia immediately denounced the claim as absurdity. South Ossetian officials as well as two Georgian opposition politicians also suggested that the Georgian authorities might have been behind the incident.
On September 24, 2007, the Russian ambassador to Georgia, Vyacheslav Kovalenko, became embroiled in a controversy over his statement at a televised informal meeting with Georgian intellectuals organized by the Tbilisi-based Russian-Georgian Friendship Union in which he referred to the Georgian people as a "dying-out nation", and announced to the Georgians that they will soon became extinct in the face of globalization while Russia is "a large country, a huge country. It can digest this. You, the Georgians, will fail to digest this."
The statements sparked a public outrage in Georgia and Kovalenko was summoned by Georgia's Ministry of Foreign Affairs for explanations while the opposition factions in the Parliament of Georgia demanded the withdrawal of Kovalenko from Georgia. Georgian Parliamentary Chairperson, Nino Burjanadze, responded to the ambassador’s prediction: "Maybe, certain forces in Russia really want to see the extinction of Georgian nation, but this will not happen… I would advice Mr. Kovalenko to think about Russia and its demographic problems and we will ourselves take care of Georgian problems, including the demographic ones."
In a televised address on the day of clashes between protesters and police in Tbilisi on November 7, 2007, Saakashvili said his country faced "a very serious threat of unrest". "High ranking officials in Russian special services are behind this," he said, adding that he had evidence. He said several Russian diplomats would be expelled from Georgia for engaging in "espionage". Earlier he had recalled Georgia's ambassador to Moscow, Irakly Chubinishvili, for "consultations".
"Moscow regards the latest idiocy by Georgian authorities as political irresponsible provocation. An appropriate response will be made, and Russia will remain true to its commitments regarding assisting in the settlement of the Georgian-Abkhazian and Georgian-Ossetian conflicts and the protection of Russian nationals living there," the Russian Foreign Ministry statement said.
On April 20, 2008 a Georgian unmanned aerial vehicle (UAV) was shot down over the Abkhazian conflict zone. Abkhazia's separatist administration immediately said its own forces shot down the drone because it was violating Abkhaz airspace and breached ceasefire agreements. Garry Kupalba, deputy defence minister of the unrecognised Republic of Abkhazia, told reporters the drone had been shot down by an "L-39 aircraft of the Abkhaz Air Force". He also identified the drone as an Israeli-made Hermes 450.
However, Georgia's defence ministry released video the next day showing what appears to be a Russian MiG-29 shooting down the unarmed Georgian drone. The video, shot from the drone moments before impact, shows a jet launching a missile over what appears to be the Black Sea. Moscow denied Georgia’s accusation and stressed that none of its planes were in the region at the time.
Furthermore, Russian Ministry of Foreign Affairs issued a statement accusing Georgia of violating 1994 Moscow agreement and United Nations resolutions on Abkhazia by deploying without authorisation a UAV (which also can be used to direct fire) in the Security Zone and the Restricted Weapons Zone.