Tensions between Moscow and Tbilisi have seen a new deterioration since the Russian leadership called for closer ties with Abkhazia and South Ossetia, another breakaway Georgian republic, in mid-April.
Until the Russian presidential order on closer ties with the regions, "which infringes upon Georgia's rights, is revoked, it will be an obstacle to Russia's WTO accession," Temuri Yakobashvili said.
Russia has been seeking membership of the global trade body since 1993. So far, Moscow has concluded bilateral talks with over 60 states, but still needs to complete discussions with two WTO members - Saudi Arabia and Georgia.
Earlier in May Georgia refused to continue talks on Russia's WTO bid over Russia's support for Abkhazia and South Ossetia, which Georgia says Russia is trying to annex.
Tbilisi vetoed Russia's accession to WTO last year. Relations between the two former Soviet republics have been in continual decline ever since the Western-leaning Mikheil Saakashvili came to power in Georgia in 2004.
Moscow's chief WTO negotiator Maxim Medvedkov earlier said that Georgia's demand that Moscow withdraw its support for Abkhazia and South Ossetia had not hampered the latest round of multilateral talks. He also said Russia could complete bilateral and multilateral talks on its WTO accession and join the body by the end of the year.