The border deals, which Russian President Dmitry Medvedev signed with the two republics at a ceremony in the Kremlin on Thursday, have been condemned by NATO for being a "clear contravention" of a French-brokered cease fire agreement.
"Border guard units...have started their duties on protecting the borders in Abkhazia and South Ossetia," Sergei Livantsov said without giving details of how many personnel were involved in the operations.
Russia recognized Abkhazia and South Ossetia as independent states after a brief war with Georgia.
The border agreement comes at a time of heightened tensions between Moscow and the military alliance, following planned NATO exercises in Georgia due to start later in the week and the expulsion of two Russian NATO envoys over spying claims.
The NATO exercises have been slammed by Russia despite reassurances that they will not involve light or heavy weaponry. Some 19 NATO countries and 1,300 troops are expected to participate, although Serbia, Moldova and Kazakhstan have withdrawn.
Russian president Dmitry Medvedev said earlier, "NATO's plans to hold exercises in Georgia...are an open provocation. Exercises must not be held there where a war has been fought," and warned that the exercises could have negative consequences for those who made the decision to hold them.
NATO announced the expulsion of the two Russian diplomats, one of whom is the son of Russia's EU envoy Vladimir Chizhov, on Thursday. The move follows a spy scandal involving an Estonian official, Herman Simm, who was jailed for 12 years for handing over secret documents to Russian intelligence operatives.
Russia's foreign ministry called the move "scandalous" and added "Naturally, we will draw our own conclusions about this provocation."
According to Nesterenko, the new borders agreements, "are designed to strengthen security and stability in the region, and do not interfere with the current search for acceptable formats of international presence [in the region]."
Under the agreements, Russia will guard the Abkhaz and South Ossetian borders, including maritime frontiers, until both republics form their own border guard services. The agreements, for an initial five years, can be renewed upon their expiration.