Medvedev signed decrees to recognize the independence of the two Georgian separatist republics earlier in the day.
He instructed the Foreign Ministry to open negotiations with the South Ossetian and Abkhazian sides on drafting a treaty of friendship, cooperation and mutual assistance, and submit it for signing.
Pending the treaties, the president ordered the Defense Ministry to ensure peace enforcement in the separatist provinces, following a request from their presidents, the Kremlin press service said.
Abkhazia's president said his country would soon sign a military cooperation agreement with Russia.
"These documents will be signed in the near future. We proposed signing a military cooperation agreement even before the recognition," Sergei Bagapsh said.
Asked whether Abkhazia feared ending up in international isolation following the recognition of its independence by Russia, he said that the republic's leadership "takes a realistic view of the situation."
Both houses of Russia's parliament voted unanimously Monday on a resolution asking the president to recognize the independence of Abkhazia and South Ossetia, following requests from the leaders of both breakaway republics.
The move will further worsen Russia's relations with the West, already strained over Moscow's response to Georgia's attack earlier this month to retake South Ossetia.
U.S. President George W. Bush and German Chancellor Angela Merkel warned Medvedev against the move on Monday, urging him to respect Georgia's territorial integrity.
Russian officials have said Georgia lost its right to the two regions after launching a military offensive that killed hundreds of people and forced thousands to flee devastated South Ossetia.
