At a press conference on November 13, 2006, Kokoity termed Sanakoyev and Karkusov, head of the alternative election commission and a former adviser to Kokoity, "traitors to their homeland and traitors to the South Ossetian people." The South Ossetian media launched a campaign to discredit and compromise Sanakoyev, accusing him of corruption, duplicity, and collaborating with Georgian intelligence.
In December 2006, Sanakoyev formed a government, choosing not to appoint a defense minister.[4]
On May 10, 2007, Sanakoyev was appointed by the President of Georgia as the Head of South Ossetian Provisional Administrative Entity. The next day Sanakoyev addressed the Parliament of Georgia in Ossetic, outlining his vision for a resolution of the conflict in South Ossetia (full text).[5] The move earned praise from the United StatesState Department, but alarmed the de facto authorities in Tskhinvali, which ordered the blocking of traffic to ethnic Georgian villages and threatened to oust Sanakoyev’s government by force, moves that received the disapproval of the Russian government.[6]
On June 26, 2007, Sanakoyev delivered a speech, in his native Ossetian, at the EU-Georgian Parliamentary Cooperation Committee in Brussels, his first appeal to the international community. He emphasized that "a direct dialogue between the Georgian and Ossetian peoples, and demilitarization of the region, are of crucial importance... The European type of autonomy, like in South Tyrol, can serve as a model... in unified Georgia... where liberal democracy is being built".[7]
On July 3, 2008, Sanakoyev survived an attack on the convoy he was traveling in when it hit a remote-controlled mine. Both Sanakoyev’s administration and Georgian police officials blamed forces loyal to Kokoity's separatist government of South Ossetia for organizing the incident, but a representative of that government denied any connection with the attack.[8]