Col. Igor Konashenkov said that a motorized infantry battalion, comprising 500 Russian troops and military equipment, was replaced in line with a May 1994 ceasefire agreement and a mandate on peacekeeping operations in the conflict zone.
"A train carrying Russian peacekeepers who spent a year in the [Georgian-Abkhazian] conflict zone departed to Russia at 09.30 Moscow time [05.30 GMT]," Konashenkov said.
Abkhazia is one of Georgia's two breakaway de facto independent republics, along with South Ossetia, which broke away from Georgia following the collapse of the Soviet Union.
Russian peacekeepers have been deployed in the republics since the 1990s. Moscow recently bolstered the number of its peacekeepers in Abkhazia to 2,500 in response to a Georgian troop build-up, but said the increase was still within previously agreed limits of 3,000 soldiers.
Relations between Moscow and Tbilisi have drastically deteriorated since Russia's former president Vladimir Putin called for closer ties between Moscow and the two breakaway republics in mid-April.
Georgia has accused Russia of trying to annex Abkhazia and South Ossetia, while Moscow says Tbilisi is planning to invade Abkhazia.
On Saturday, a battalion of Russian Railroad Troops arrived in Abkhazia to repair a stretch of railroad between Sukhumi and Ochamchira.
The Abkhazian authorities confirmed the arrival of Russian troops but said it was part of humanitarian aid declared by former Russian president Vladimir Putin in mid-April and had "nothing to do with the situation in the Georgian-Abkhaz conflict zone."