The regions have called for international recognition of their self-declared independence, citing Kosovo's decision last month to break away from Serbia as a precedent.
Rogozin underlined that a national referendum on whether to join Nato organised in December by Mikheil Saakashvili, Georgia's president, was not held in its two breakaway republics.
The ambassador said on Tuesday: "This is why I think that if Nato accepts that Georgia takes part in the Membership Action Plan (Map), that this could provoke the secession of the two territories.
"This would be enough for the separatists to go through with secession."
The Map programme, seen as a preliminary to Nato membership, helps aspiring countries meet alliance standards and prepares them to join.
Rogozin said: "It is a very dangerous process because it could reheat the conflict. All this is of concern to us, because it's happening near our borders.
"Many citizens of the northern Caucasus have links with South Ossetia and Abkhazia."
Elene Khoshtaria, Georgia's deputy minister for European and Euro-Atlantic integration, said that Russia was trying to blackmail Georgia into not joining Nato.
She said: "The statement... is nothing but an attempt to blackmail allied nations and Georgia. Georgia's Nato membership bid is not against Russia, it's about our dedication to the common values of democratic nations.
"I am confident that Nato member states will make a decision on Georgia's membership independently and that third-party blackmail cannot hamper this process."
Meanwhile, the United States said on Tuesday that it regretted Russia's decision last week to lift trade sanctions imposed on Abkhazia and reaffirmed its support for Georgia's territorial integrity.
The Russian sanctions were imposed in 1996 as part of efforts to limit
the separatist aspirations of Abkhazia.
Zalmay Khalilzad, the US ambassador to the United Nations, said: "The United States regrets Russia's decision to withdraw unilaterally from the CIS (Commonwealth of Independent States) sanctions on Abkhazia.
"We do not see how it contributes to stability in the South Caucasus, resolution of the Abkhazian conflict or improvement of Russian-Georgian relations.
Moscow said it was lifting the trade restrictions but denied it had been influenced by Western support for Kosovo's independence.
The Russian foreign ministry said that Moscow "no longer considers itself bound by the terms" of a sanctions accord approved by the ex-Soviet CIS in 1996.
Vladimir Putin, Russia's outgoing president, has accepted an invitation to a Nato summit in Bucharest, the Romanian capital, in April.