At the Georgian airport in Tbilisi, protesters waved signs reading "you are not welcome" as the first direct flight from Russia arrived.
As authorities forbade them from standing outside the airport arrivals area, fights broke out.
Azimuth Airlines' aircraft landed at 13:20 local time (09:20 BST), many days after Georgia's civil aviation authorities gave it the all-clear.
The administration of Georgia has praised the arrival of direct flights from Russia once more.
Irakli Kobakhidze, the leader of the ruling Georgian Dream party, claimed that "the beneficiaries are our citizens who have to take a detour at a triple the cost."
Although Russian statistics indicate that the number is more likely closer to 114,000, the administration claims that a million ethnic Georgian nationals who reside in Russia stand to gain.
However, the majority of Georgians disagree with the government's decision to permit flights, and more than 100 Georgian organizations claim it is a "direct sabotage" of their nation's efforts to join the EU. Georgia expects Brussels to accept its application to be a candidate later this year.
According to Russia's state news agency, a group of pro-Russian Georgian NGOs and companies were on board the first flight. Additionally, Georgian Airways intends to offer daily flights to Moscow.
The apparent warming of relations follows President Vladimir Putin's signing of a decree lifting Moscow's unilateral ban on direct flights, which was put in place in reaction to pro-Russian demonstrations in Tbilisi in 2019.
The 20-year-old ban on Georgian nationals entering Russia has also been repealed, enabling them to travel there for up to 90 days without a visa.
Yet there are no official ties between the two nations.
Following their 2008 conflict, Russia still occupies 20% of Georgia's internationally recognized territory.
Salome Zurabishvili, the pro-European president of Georgia, condemned "yet another Russian provocation."
And the recent developments have been met with dissatisfaction from the US and the EU.
Kelly Degnan, the US ambassador to Georgia, questioned the wisdom of accepting "a gift" from what she referred to as an aggressor nation.
The crucial query, in my opinion, is why, why now? Why is Putin now giving Georgia these incentives and concessions? What will Georgia be required to pay as a result?
We all understand that Putin never gives something away without getting something in return, she claimed.
The decision raised questions about Georgia's willingness to joining the 27-member union, according to Peter Stano, the EU's spokesperson for international affairs, who made the statement earlier this week.
"We and our partners do not allow flights from Russia, flights to Russia, or flights over Russia," he said.
The restoration of direct flights as a "reward" for the Georgian Dream government's "good behavior" toward Russia during its invasion of Ukraine has been roundly criticised by the country's opposition.
Tens of thousands of Russian people were permitted to come here by Georgia, which did not apply sanctions against Russia and did so while allowing many of them to avoid mobilization.
The head of the largest opposition group, the United National Movement, Levan Khabeishvili, claimed that President Putin was attempting to transform Georgia into a "Russian province."
But he said, "The Georgian people's will is unwavering! We opt for Europe over Russia.
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