The population of Montenegro is mostly Orthodox Slavs and Moscow has long considered it to be in its sphere of influence.
The decision by US President Donald Trump to sign off on the accession by the Balkan country to the North Atlantic Treaty Organisation on Tuesday "reflects the logic of confrontation on the European continent and creates new dividing lines," the ministry said in a statement.
"We consider the course towards including Montenegro in NATO is deeply erroneous, goes fundamentally against the interests of people in this country and harms stability in the Balkans and in Europe as a whole," it said.
It added that the accession was forced upon Montenegro through what it called "puppet NGOs" that work to "create the illusion of public support for the one-sided policy of the Montenegrin authorities."
The population of Montenegro, on the Adriatic Sea, is mostly Orthodox Slavs and Moscow has long considered it to be in its sphere of influence.
The White House on Wednesday moved to accuse Moscow of being behind an attempted coup during Montenegro's October elections, which saw a group of Serbian nationals jailed last month.
The country hopes to become a NATO member later this year, which would reinforce the bloc's presence in the Balkans as Greece, Croatia and Albania are already members.