Ferries between the two cities were stopped in 1992 during the Georgian-Abkhaz conflict, in which between 10,000 and 30,000 people died and tens of thousands more fled their homes.
In the late 1990s, Russia restarted passenger services to the breakaway republic's capital, Sukhumi.
"We have a great hope that the sea link popular in the Soviet times will be profitable now," the spokesman said of the Sochi-Gagra route.
The high-speed ferries take 45 minutes for the trip between Sochi and Gagra and can carry up to 189 passengers.
Georgia warned last week that setting up regular sea links with Abkhazia was internationally prohibited. Tbilisi officially closed all ports in Abkhazia after the republic broke away from Georgia in the early 1990s.
The resumption of the Sochi-Gagra ferries came shortly after the Black Sea resort was rocked by two explosions injuring six people on Sunday. Coupled with two more bombings in Sukhumi on Monday, that prompted the Abkhaz authorities to partially close its administrative border with Georgia on Tuesday.
Abkhaz President Sergei Bagapsh blamed Georgia for the bombings. Tbilisi called the accusations "absurd."
Relations between Russia and Georgia have been strained since Russia stepped up support for Abkhazia and South Ossetia, another breakaway Georgian republic. The pro-Western government of Georgian President Mikheil Saakashvili has said it is determined to bring the breakaway regions back under its control, while Moscow says Tbilisi's policies could lead to new bloodshed.
