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"Border guard units ...have started their duties on protecting the borders in Abkhazia and South Ossetia," the RIA Novosti news agency quoted Sergei Livantsov as saying.
Livantsov did not specify the number of personnel deployed in the operations.
Earlier leader of South Ossetia Eduard Kokoity said Russian boarder guards have entered South Ossetia and are monitoring its border with Georgia, the Interfax news agency reported.
Border defense agreements were signed by Russian President Dmitry Medvedev, Kokoity and Sergei Bagapsh, leader of Abkhazia, on Thursday in the Kremlin.
Under the agreements, the two regions will delegate to Russia their border guard duties, including those of maritime frontiers, until they establish their own border guard agencies.
The pacts are effective for five years and are renewable up expiration.
Russia will also help train personnel and set up border guard agencies for Abkhazia and South Ossetia, the Itar-Tass news agency said.
Georgia launched an assault on South Ossetia last August. Russia responded with a counter-offensive involving tanks and troops, which quickly drove Georgian forces back after a five-day war.
On Aug. 12, 2008, Medvedev announced the end of military operations in South Ossetia, and agreed with his French counterpart Nicolas Sarkozy on six principles for settlement of conflict in the region. Russia then recognized South Ossetia and Abkhazia as independent states on Aug. 26.
Georgia has strongly condemned the pacts, said a statement issued by the Georgian Foreign Ministry on Friday.
However, Russia insists that it has never reached cease-fire agreements with Georgia, the only agreements it abides by is the "Medvedev-Sarkozy plan," said Russian Foreign Ministry spokesman Andrei Nesterenko in a statement.