The European Union criticised the resumption, which comes amid a sharp warming in relations between Russia and Georgia, countries that have had no formal diplomatic ties since Russia routed Tbilisi's forces in a brief war in 2008.
Tbilisi has in recent months tried to balance rapprochement with its giant neighbour and its aspirations to join the European Union.
Georgia was rocked by protests in March after lawmakers moved to adopt a Russian-style bill requiring non-government organisations receiving more than 20% of their funding from abroad to register as "agents of foreign influence".
Brussels said the plan was incompatible with EU membership and the bill was later withdrawn.
The EU said on Tuesday it regretted that Georgia was resuming flights to Russia at a time when the bloc has closed its airspace to Russian planes in response to Moscow's invasion of Ukraine.
"This latest decision by Georgia's authorities raises concerns in terms of Georgia's EU path," EU foreign affairs spokesman Peter Stano said in a briefing.
The Civil Aviation Agency said there would be seven flights a week to Moscow. Georgian Airlines did not immediately respond to a request for comment.
(Reporting by Reuters; Writing by Caleb Davis; Editing by Kevin Liffey)
